Source: http://www.timelogic.com/papers-citing-timelogic-products
Timestamp: 2019-04-22 18:58:04+00:00

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The following articles reference the use of TimeLogic's DeCypher® and CodeQuest® bioinformatics systems. Click on the links to view abstracts or full text where available.
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Identification of salt stress response genes using the Artemia transcriptome.
"Then, all transcript contigs and all singletons longer than 500 bp were selected for functional annotation with BLAST (TimeLogic® Tera-BLASTp™ algorithm Active Motif Inc., Carlsbad, CA, default parameters, NRProt database)."
The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization.
The Role of Trehalose 6-Phosphate in Crop Yield and Resilience.
"In addition, the wheat protein sequences belonging to the TGACv1 wheat reference (Clavijo et al., 2017) were improved (Supplemental Tables S5 and S6) by performing BLAST searches in an in-house TimeLogic DeCypher server (tera-blastp, max_scores = 10, e-value ≥ 1–5) against the high-confidence IWGSC RefSeq v1.0 proteins (available under Toronto agreement). Using this methodology, we have identified 25 wheat TPS proteins (Supplemental Tables S7 and S9) and 33 TPPs (Supplemental Tables S8 and S10)."
Inter-genome comparison of the Quorn fungus Fusarium venenatum and the closely related plant infecting pathogen Fusarium graminearum.
"Blast2GO V.3.1 was used with Decypher BLASTP searches with an E-value of 0.001 against the NCBI nr database from 27/06/15, filtered using blast2go annotation algorithm with settings, E-value filter 0.000001, Annotation CutOff 55, GO weight 5, Hsp-Hit Coverage CutOff 0, and GO and enzyme code annotated using a local GO database from 07/2015.."
Genomic, Biochemical, and Modeling Analyses of Asparagine Synthetases from Wheat.
"Genomic Analysis: DeCypher Tera-BLASTN Search Nucleic Query vs. Nucleic Database was used to assess the wheat asparagine synthetase gene sequences."
Suppression of a single BAHD gene in Setaria viridis causes large, stable decreases in cell wall feruloylation and increases biomass digestibility.
de Souza, W. R., Martins, P. K., Freeman, J., Pellny, T. K., Michaelson, L. V., Sampaio, B. L., Vinecky, F., Ribeiro, A. P., da Cunha, B. A. D. B., Kobayashi, A. K., de Oliveira, P. A., Campanha, R. B., Pacheco, T. F., Martarello, D. C. I., Marchiosi, R., Ferrarese-Filho, O., dos Santos, W. D., Tramontina, R., Squina, F. M., Centeno, D. C., Gaspar, M., Braga, M. R., Tiné, M. A. S., Ralph, J., Mitchell, R. A. C. and Molinari, H. B. C.
"To identify orthologs in the 1,000 Plants (1KP) database of plant transcriptomes (Wickett et al., 2014), we identified all hits with E < 10-5 using nucleotide Blast (Blastn) (Matasci et al., 2014) with rice candidate genes as queries; these were downloaded and assigned as ortholog of top rice hit if the bit score was > 100 using translated nucleotide searches against the rice proteome with Tera-Blastp on the DeCypher® platform."
Identification and expression profiling of Pht1 phosphate transporters in wheat in controlled environments and in the field.
Grün, A., Buchner, P., Broadley, M. R. and Hawkesford, M. J.
"Identification of wheat TaPht1 genes and phylogenetic analysis: Putative members of the Pht1 gene family in Triticum aestivum were identified based on Pht1 gene sequences from barley (HvPht1; Rae et al. 2003), Brachypodium distachyon (BradiPht1; Hong et al. 2012) and rice (OsPht1; Paszkowski et al. 2002) by BLAST analysis with a cut-off threshold of 0.0001–0.01 (Altschul et al. 1990) using available wheat genome databases on the EnsemblePlant (Kersey et al. 2016), PLAZA3.0 (Proost et al. 2015) and the Rothamsted decypher web interface platforms [wheat databases: IWGSC (2014), TGAC (TGACv1 genome assembly of Triticum aestivum cv. Chinese Spring, generated by The Genome Analysis Centre, Norwich, as part of the BBSRC-funded project, Triticeae Genomics for Sustainable Agriculture) and other wheat varieties (opendata.earlham.ac.uk/Triticum_aestivum/EI/v1 www.earlham.ac.uk/sequencing-wheat-genome)]."
The Plastid Genome in Cladophorales Green Algae Is Encoded by Hairpin Chromosomes.
Del Cortona, A., Leliaert, F., Bogaert, K.A., Turmel, M., Boedeker, C., Janouškovec, J., Lopez-Bautista, J.M., Verbruggen, H., Vandepoele, K., De Clerck, O.
"The resulting contigs (hereafter, transcripts) were compared using sequence similarity searches against the NCBI non-redundant protein database using Tera-BLAST(TM) DeCypher (Active Motif, USA). [...} Transcripts classified as "eukaryotic" were further examined to assess transcriptome completeness and to identify chloroplast transcripts. These transcripts were analysed using Tera-BLAST(TM) DeCypher against Chloroprotein_db."
Old meets new: most probable number validation of metagenomic and metatranscriptomic datasets in soil.
Mauchline, T.H., Hayat, R., Clark, I.M. and Hirsch, P.R.
"To estimate the number of nodA and nodD genes and transcripts we used Decypher BLAST (Time Logic®) to interrogate the metagenomes and metatranscriptomes with full-length R. leguminosarum sv. trifolii WSM 1689 gene sequences derived from NCBI (https://www.ncbi.nlm.nih.gov/)."
A conserved fungal glycosyltransferase facilitates pathogenesis of plants by enabling hyphal growth on solid surfaces.
"RNA sequencing and differential gene expression analysis: [...] Annotations were added to the cuffdiff output using Blast2Go (v3.3.5) with Blast2Go GO database 05/2016 and default filtering settings, using input from InterPro (v58.0) and Timelogic DeCypher with the NCBI NR database (23/06/16) using an e-value threshold of 1e-2. For robust differential expression analysis, only genes with fold changes of Log2 >1.5 (Padj 0.05) were considered further.."
Massive Protein Import into the Early-Evolutionary-Stage Photosynthetic Organelle of the Amoeba Paulinella chromatophora.
Analyses of 16S rRNA and cpn60 gene sequences provide complementary information about potentially useful and harmful oil field microbiota.
"The remaining sequences were compared against the non-redundant SSURef data set of SILVA102 (Pruesse et al., 2007) using the Tera-Blast algorithm (Active Motif)."
Genome Biology201718:28. DOI: 10.1186/s13059-017-1151-0. Published: 14 February 2017.
"Pfam domains were assigned using v. 22 of the database and a TimeLogic Decypher machine and an e-value of 10–4."
Genome and methylome of the oleaginous diatom Cyclotella cryptica reveal genetic flexibility toward a high lipid phenotype.
Biotechnol Biofuels. 2016; 9:258. doi: 10.1186/s13068-016-0670-3 Published online 2016 Nov 25.
"Functional annotation of genes from C. cryptica and the five other reference diatom genomes was performed using PhyloDB, a comprehensive database of proteins at JCVI. KEGG, KO, KO Pathway, EC annotations were assigned using TimeLogic® Tera-BLAST™ algorithm (Active Motif Inc., Carlsbad, CA, USA), e value threshold 1e-5; Pfam/TIGRfam using Hmmer v 3.1b2 (http://hmmer.org), and transmembrane domains with TMHMM 2.0c."
Genome and transcriptome sequencing characterises the gene space of Macadamia integrifolia (Proteaceae).
BMC Genomics 2016 17:937 DOI: 10.1186/s12864-016-3272-3 Published: 17 November 2016.
"...reciprocal searches of protein sequences for five enzymes (CYP79, CYP71, UGT85, beta-glucosidase and HNL) involved in CG biosynthesis from known cyanogenic plants were conducted with a DeCypher Tera-BLASTP search against all macadamia gene models."
Assembly of C. elegans acentrosomal spindles occurs without evident MTOCs and requires microtubule sorting by KLP-18/kinesin-12 and MESP-1.
Mol. Biol. Cell. Published online before print August 24, 2016, doi: 10.1091/mbc.E16-05-0291.
"Divergence tree of MESP-1 paralogs from five Caenorhabditis species (C. elegans, C. species 9, C. briggsae, C. remanei, and C. brenneri) based on a ClustalW alignment (generated using the TimeLogic DeCypher server at Stanford University) of the regions corresponding to the C-terminal 65 amino acids from C. elegans MESP-1. The tree structure indicates that paralogs arose both via gene duplication events occurring specifically in the C. briggsae, C. remanei, and C. brenneri lineages and via earlier gene duplication events that occurred prior to divergence of C. briggsae and C. species 9 (aka C. nigoni)."
Intact polar diacylglycerol biomarker lipids isolated from suspended particulate organic matter accumulating in an ultraoligotrophic water column.
Organic Geochemistry, Volume 100, October 2016, Pages 29–41.
Representing and querying disease networks using graph databases.
BioData Mining (2016) 9:23. Published: 25 July 2016.
"Sequence similarity was determined by running all versus all Tera-BlastP for the UniProt Human reference proteome on the Timelogic DeCypher system. The significance threshold was 1e-05, with effective database size adjusted to 16.9 bln bases."
Carnivorous Nutrition in Pitcher Plants (Nepenthes spp.) via an Unusual Complement of Endogenous Enzymes.
J. Proteome Res., Publication Date (Web): July 20, 2016.
"The translated database was filtered for polypeptide >150 amino acids in length and initial annotation was based on comparison with NCBI nt, NCBI nr and SwissProt databases using Tera-Blast with an e-value cutoff of e-15."
Enrichment and identification of biosurfactant-producing oil field microbiota utilizing electron acceptors other than oxygen and nitrate.
Journal of Biotechnology. Available online 19 May 2016.
"The remaining high-quality sequences were compared against the non-redundant SSURef data set of SILVA102 (Pruesse et al., 2007) using Tera-Blast (Active Motif, Inc.)."
Nature (2016) doi:10.1038/nature16548. Published online 27 January 2016.
"Gene family comparisons Protein sets were collected for 14 species: Z. marina (ORCAE v. 2.1), Arabidopsis thaliana (TAIR10), Thellungiella parvula (http://thellungiella.org) Populus trichocarpa (Phytozome v. 9.0), Vitis vinifera (Phytozome v. 9.0), Amborella trichopoda (http://amborella.huck.psu.edu), Oryza sativa japonica (Phytozome v. 9.0), Zea mays (Phytozome v. 9.0), Brachypodium distachyon (Phytozome v. 9.0), Spirodela polyrhiza (http://mocklerlab.org), Selaginella moellendorffii (Phytozome v. 9.0), Physcomitrella patens (Phytozome v. 9.0), Chlamydomonas reinhardtii (Phytozome v. 9.0), and Ostreococcus lucimarinus (ORCAE v. 6/3/2013). These species were selected in order to provide a phylogenetic representation traversing green algae, basal plants, monocots, and dicots. Following an ‘all-vresus-all’ TimeLogic Decypher Tera-BLASTP (Active Motif Inc.; e-value threshold 1e-3, max hits 500) comparison, OrthoMCL (v. 2.0; mcl inflation factor 3.0) was used to delineate gene families."
Neuropeptidergic Signaling in the American Lobster Homarus americanus: New Insights from High-Throughput Nucleotide Sequencing.
"Transcriptome mining: Searches of the H. americanus transcriptome described above were conducted on a TimeLogic DeCypher server using a protocol modified from several recent publications [40,82–84]. Specifically, the lobster assembly was selected as the database to be searched using the DeCypher Tera-BLASTP algorithm, and a known neuropeptide precursor or receptor was input to the program as the protein query. The complete list of pre/preprohormones searched for, as well as the specific queries used, is provided in Table 1; the full list of receptors searched for (and the query proteins used) is provided in Table 3. All hits returned by a given Tera-BLASTP search were fully translated using the “Translate” tool of ExPASy (http://web.expasy.org/translate/) and then checked manually for homology to the query sequence. The BLAST-generated maximum score and E-value for each of the transcripts identified as encoding a putative neuropeptide precursor or receptor are also provided in Tables 1 and 3."
Mol Biol Evol (2015) doi: 10.1093/molbev/msv337. First published online: December 10, 2015.
"To assess gene family enrichment in Agaricomycetes we used MCL clustering (11917018) with an inflation parameter of 2.0 to identify protein families in the full comparative set of organisms. This allowed the identification of Agaricomycete-specific gene families. Protein functions were then assigned by assigning the protein sequences to protein domains in the Pfam v22 database (24288371) using a TimeLogic Decypher machine."
Roles of Thermophiles and Fungi in Bitumen Degradation in Mostly Cold Oil Sands Outcrops.
Appl. Environ. Microbiol. AEM.02221-15; Accepted manuscript posted online 24 July 2015.
"The Tera-Tblastn algorithm on the TimeLogic Decypher System was used to screen fungal P450 and lignin and manganese peroxidases gene reference sequences obtained from the Fungal Cytochrome P450 Database and the Fungal Peroxidase Database against the quality controlled metagenome reads."
"Functional genes encoding proteins involved in hydrocarbon degradation and methane cycling were sought in the remaining high-quality metagenomic reads using hidden Markov models (HMMs) with the Frame Shirt Tolerance algorithm on a TimeLogic Decypher system (Active Motif, Inc.)."
The completed genome sequence of the pathogenic ascomycete fungus Fusarium graminearum.
BMC Genomics 2015, 16:544. doi:10.1186/s12864-015-1756-1. Published: 22 July 2015.
"Blast2GO V.2.7.2 was used with Decypher BLASTP search’s with an E-value of 0.001 against the NCBI nr database from 04/09/14 and 15/09/14 NCBI nr database for the 412 new gene and modified protein sets respectively, filtered using Blast2GO annotation algorithm with settings, E-value filter 0.000001, Annotation CutOff 55, GO weight 5, Hsp-Hit Coverage CutOff 0, and GO and enzyme code annotated using a local GO database from 07/2014 with 41,436 GOs available and 4,098 Enzymes available."
Cultivation of Environmental Bacterial Communities as Multispecies Biofilms.
Springer Protocols Handbooks. 04 Jun 2015. p. 1-20.
"Further screen high-quality sequences for problematic, chimeric, and eukaryotic sequences using the Tera-BLAST algorithm on the TimeLogic Decypher system (Active Motif Inc.)."
Glutathione S-Transferase (GST) Gene Diversity in the Crustacean Calanus finmarchicus – Contributors to Cellular Detoxification.
PLoS ONE 10(5): e0123322. doi:10.1371/journal.pone.0123322. Published: May 6, 2015.
"In silico transcriptome mining: Searches of the C. finmarchicus de novo assembly for putative GST-encoding transcripts were conducted using the tera-tblastn algorithm of DeCypher Tera-BLASTP on a TimeLogic DeCypher server; detailed descriptions of the search method are provided in Christie et al. and Lenz et al. Known GST proteins, the majority from the copepod T. japonicus, were used as the query sequences for all tera-tblastn searches. GST proteins from the insect D. melanogaster and the daphnid D. pulex were used as queries to search for the cytosolic Epsilon GST subclass (insect specific) and the mitochondrial Kappa class, respectively. Lastly, the nucleotide sequences of five C. finmarchicus expressed sequence tags (ESTs) previously identified as encoding putative GSTs were used as queries to search the de novo transcriptome using the tera-tblastx algorithm. The default parameters of both tera-tblastn and tera-tblastx were used for all searches."
Whole-genome analysis of Fusarium graminearum insertional mutants identifies virulence associated genes and unmasks untagged chromosomal deletions.
Urban, M., King, R., Hassani-Pak, K., & Hammond-Kosack, K. E.
BMC Genomics, 16(1), 261. Published 3 April 2015.
"A custom BLAST database was setup and implemented on a TimeLogic® Tera-BLAST™ DeCypher system (Active Motif Inc., Carlsbad, CA). For each gene the top BLAST hit (E-value of ≥10E-4) with annotation including the experimentally tested phenotypes was extracted."
Transcriptome Profiling of Khat (Catha edulis) and Ephedra sinica Reveals Gene Candidates Potentially Involved in Amphetamine-Type Alkaloid Biosynthesis.
Groves, Ryan A., Jillian M. Hagel, Ye Zhang, Korey Kilpatrick, Asaf Levy, Frédéric Marsolais, Efraim Lewinsohn, Christoph W. Sensen, and Peter J. Facchini.
PloS one, 10(3), e0119701. March 25, 2015.
"The TimeLogic Tera-BLAST algorithm (http://www.timelogic.com) was used to compare transcripts to the NCBI database NR (non-redundant) and the viridiplantae subset of RefSeq. An expected e-value of 1e-3 and a minimum alignment length of 30 bp were used."
Rhizobiales as functional and endosymbiontic members in the lichen symbiosis of Lobaria pulmonaria L.
Front Microbiol. 2015; 6: 53. Published online 2015 Feb 10. doi: 10.3389/fmicb.2015.00053.
"To obtain taxonomic assignments, the Tera-BLASTN program (www.timelogic.com) was run on the 368,424 contigs, using TimeLogic (Active Motif, Carlsbad, CA, USA) DeCypher boards against the “nt” (nucleotide sequence) database from NCBI (ftp://ftp.ncbi.nlm.nih.gov/blast/db). [...] For functional analysis, we used a similar approach as above but used Tera-BLASTX (www.timelogic.com), which was run against the “nr” (non-redundant protein sequence) database from NCBI (ftp://ftp.ncbi.nlm.nih.gov/blast/db)."
Exploring functional contexts of symbiotic sustain within lichen-associated bacteria by comparative omics.
The ISME journal, 9(2), 412-424. February 2015.
"The Tera-BLASTN program was run on the 368,424 contigs, using TimeLogic (Active Motif, Carlsbad, CA, USA) DeCypher boards against the 'nt' database from NCBI (ftp://ftp.ncbi.nlm.nih.gov/blast/db)."
Microbially enhanced oil recovery from miniature model columns through stimulation of indigenous microflora with nitrate.
Kryachko, Y., & Voordouw, G.
International Biodeterioration & Biodegradation, 96, 135-143. December 2014.
"The remaining high-quality sequences were compared against the non-redundant SSURef data set of SILVA102 (Pruesse et al., 2007) using the Tera-Blast algorithm on a 16-board TimeLogic Decypher system (Active Motif, Inc.)."
Genetical and comparative genomics of Brassica under altered Ca supply identifies Arabidopsis Ca-Transporter orthologs.
The Plant Cell Online, 26(7), 2818-2830. Published online July 2014.
"Each probe set on the Affymetrix Brassica Exon 1.0 ST array was mapped to the B. rapa gene lists from the BRAD database (version 1.2; plantgdb.org/BrGDB/) (Cheng et al., 2011). A match between a probe set and a gene was created if at least one probe in that probe set had an exact, full-length, ungapped alignment to that gene. The probes were aligned using TimeLogic DeCypher Tera-BLASTN. Brassica genes most similar in sequence to a particular Arabidopsis gene were found by aligning Brassica protein sequences (BRAD version 1.2) to Arabidopsis protein sequences from TAIR (release 10; http://www.arabidopsis.org) using TimeLogic DeCypher Tera-BLASTP (e value cutoff = 10e-4). For each Brassica protein sequence, a single match was defined as the Arabidopsis sequence aligning with the highest bit score."
BMC Research Notes 2014, 7:388 doi:10.1186/1756-0500-7-388. Published 24 June 2014.
"Automatic functional annotation: For more accuracy and further variety of functional annotation, we used various annotation algorithms and public databases. First, we assigned putative functions to the CsAEs based on BLASTN (Query Coverage ≥ 80.0%, Identity ≥ 70.0%, E-value ≤ 1.0e-5), BLASTX and TBLASTX (Match No. ≥ 30 aa, Identity ≥ 25.0%, E-value ≤ 1.0e-5) searches against the GenBank NT and NR databases (ftp://ftp.ncbi.nih.gov/blast/db/FASTA/). Second, metabolic pathways are extremely important for correctly inferring pathogen invasion, host defense, adaptation, pathogen life cycle and host-pathogen interactions. To get a rationale for the development of anti-parasitic drugs and vaccines, we must identify all parasite-specific metabolic pathways. To identify the pathways, additional annotations were created against the UniProtKB database (http://www.ebi.ac.uk/uniprot) and the KEGG database (http://www.genome.jp) using BLASTX (Match No. ≥ 30 aa, Identity ≥ 25.0%, E-value ≤ 1.0e-5). All BLAST algorithms were implemented using a TimeLogic DeCypher system (Active Motif, Inc., http://www.activemotif.com)."
Improved structural annotation of protein-coding genes in the Meloidogyne hapla genome using RNA-Seq.
Worm. 2014; 3: e29158. Published online 2014 May 16. doi: 10.4161/worm.29158 PMCID: PMC4165543.
"To improve the reliability of gene predictions, the TimeLogic GeneDetective algorithm (Active Motif Inc.) was employed to yield the HapPep3 release. The algorithm reconstructs splice junctions in order to accurately align EST/cDNAs, proteins, or uses Hidden Markov Models to genomic DNA to produce a graphical gene model."
Nature Communications 5, Article number: 3745. Published 09 May 2014.
"All predicted gene models were functionally annotated by alignment similarity to annotated genes from the GenBank NR using BLASTp and hardware-accelerated double-affine Smith-Waterman alignments (deCypherSW; http://www.timelogic.com/decypher_sw.html) against SwissProt (http://www.expasy.org/sprot), the Kyoto Encyclopaedia of Genes and Genomes (KEGG), and eukaryotic orthologous groups of proteins (KOG)."
"Searches of the transcriptome assembly produced by Trinity were conducted using the DeCypher Tera-BLASTP algorithm on the Mount Desert Island Biological Laboratory's TimeLogic DeCypher server (MDIBL, Salisbury Cove, ME, USA)."
Active removal of inorganic phosphate from cerebrospinal fluid by the choroid plexus.
Am J Physiol Renal Physiol 306:F1275–F1284, 2014. First published April 16, 2014; doi:10.1152/ajprenal.00458.2013.
"Pi transporter expression and localization: Data “mining” of the MDIBL S. acanthias expressed sequence tag database (DeCypher.MDIBL.org) identified several partial DNA sequences that showed considerable conservation with zebrafish (Danio rerio, NP_997753, NP_998344 and NP_001071014), green pufferfish (Tetraodon negroviridis, CAG08601), African clawed frogs (Xenopus laevis, NP_001083287 and NP_ 001088186), rats (R. norvegicus, NP_112410 and NP_058919), and humans (Homo sapiens, NP_005406 and NP_006740.1) PiT1 and PiT2 proteins. Two of these sequences corresponded to 76 (PiT1) and 100 (PiT2) amino acids in a very conserved region near the NH2-terminus, encompassing the extracellular domain and first and second transmembrane domains, the first (intracellular) loop and extending into part of the second (extracellular) loop (PiT1), and the third transmembrane domain (PiT2). These sequences shared 72% nucleotide and 82% protein identity and cluster differently with PiT1 and PiT2. A third fragment was found with a high correspondence to a 232-amino acid region that spans from approximately half of the seventh loop (intracellular) to the tenth loop (extracellular), thus comprising transmembrane domains seven, eight, and nine. This sequence shared considerably higher identity with the amino acid sequence of PiT1 than of PiT2 in X. laevis (72% vs. 60%), R. norvegicus (84% vs. 59%), and H. sapiens (86% vs. 59%)."
De Novo Assembly of a Transcriptome for Calanus finmarchicus (Crustacea, Copepoda) – The Dominant Zooplankter of the North Atlantic Ocean.
"the complete transcriptome assembly was downloaded to a TimeLogic DeCypher server at the Mount Desert Island Biological Laboratory (Salsbury Cove, Maine) and searched using the Tera-BLASTP algorithm for sequences that were putative homologs of a known protein query (typically ones from the fruit fly D. melanogaster)."
Secondary cell wall composition and candidate gene expression in developing willow (Salix purpurea) stems.
"RNA-seq was carried out on four samples from third internodes isolated at 0, 2, 4 and 6 weeks after transfer to soil. Library preparation and sequencing were carried out by the University of Bristol Transcriptomics Facility (Bristol, UK) using an Illumina GAiix sequencer generating 114 bp single-end reads. The libraries each generated 10–15 million reads and were quality trimmed and filtered (fastq_quality_trimmer-t 20-l 40), which discarded on average 23 % of the reads. The processed reads were mapped to the complete set of poplar genes (CDS v2.2) using TimeLogic® Tera-BLASTN™ algorithm (Active Motif Inc., Carlsbad, CA, USA) and taking the top-hit with e value <1E-20. [...] To look for willow-specific transcripts, the RNA-seq libraries were pooled and de novo assembled using Trinity (Grabherr et al. 2011) (version trinityrnaseq_r2013_08_14). In total 81,701 contigs were obtained and aligned (Tera-BLASTN™, E value <1e-5) to poplar CDS sequences."
The Genome of the Foraminiferan Reticulomyxa filosa.
"4.3.1 Global analysis of potential HGT: We examined the affiliation of all R. filosa and B. natans proteins with members from other supergroups by similarity and automated phylogenetic tree reconstructions (Figure S18). The R. filosa predicted protein models were phylogenomically analyzed as described before. The phylogenomic reference database included RefSeq (release 55) and additional sequence data for unicellular eukaryotes from different repositories e.g., NCBI nr, JGI and dbEST with a total of about 24 million protein models from more than 300,000 species and strains. Each query protein was searched for homologous sequences in the database using Tera-BLAST (blastp) on a TimeLogic® DeCypher® system (Active Motif Inc., Carlsbad, CA) with e-value threshold ≤ 1E-10. The BLAST hits were processed to provide an inclusive and unbiased taxon sampling at the different taxonomic levels, while maintaining computationally tractable alignments and phylogenetic trees."
Heterococcus sp. DN1 draft genome: focus on cold tolerance and lipid production.
Microbiome Science and Medicine. Volume 1, Issue 1 (Dec 2013).
"Reads were assembled into contigs using the assembly program ABySS. [...] The assembled genome was then used for gene prediction using the computer software Genemark (GM). [...] The GM prediction file (.hmm) was then used for a tera-BLASTX (DeCypher, TimeLogic, Carlsbad CA, http://www.timelogic.com/catalog/757) to discover orthologous peptide sequences from NCBI."
Discovery of a metabolic alternative to the classical mevalonate pathway.
eLife 2013;2:e00672, Published December 10, 2013.
"Genes were predicted from genomic sequences using Genewise (Birney et al., 2004) and TimeLogic GeneDetective (Active Motif Inc., Carlsbad, CA) programs, with manual editing."
Solution NMR studies of the plant peptide hormone CEP inform function.
FEBS Letters, Available online 5 November 2013.
"Using our deduced consensus sequence “xfrPTxpGxSPGxGx” based on the five initial Arabidopsis CEP, we interrogated our ORF database using a double-affine Smith-Waterman algorithm implemented in an accelerated TimeLogic hardware environment (TimeLogic DeCypher systems; www.timelogic.com)."
Identification and developmental expression of the enzymes responsible for dopamine, histamine, octopamine and serotonin biosynthesis in the copepod crustacean Calanus finmarchicus.
Network-Based Data Integration for Selecting Candidate Virulence Associated Proteins in the Cereal Infecting Fungus Fusarium graminearum.
"The sequence similarity network was constructed from the results of an all-versus-all sequence matching of the proteins in version 3.2 of the Fusarium annotation at (http://mips.helmholtz-muenchen.de/genre/?proj/FGDB/) implemented on a TimeLogic® Tera-BLAST™ (Active Motif Inc., Carlsbad, CA)."
Journal of Biotechnology, Available online 16 July 2013.
"To accelerate the BLAST searches (Altschul et al., 1990), which are required in several stages of the pipeline, we use hardware-accelerated TimeLogic DeCypher boards (Active Motif Inc, Carlsbad, CA) with their custom BLAST programs."
"Protein function predictions were made for all predicted gene models using a suite of bioinformatic tools: SignalP, TMHMM, InterProScan, and hardware-accelerated double-affine Smith-Waterman alignments (http://www.timelogic.com) with SwissProt, KEGG, and KOG."
Prediction of the protein components of a putative Calanus finmarchicus (Crustacea, Copepoda) circadian signaling system using a de novo assembled transcriptome.
"Searches of the transcriptome assembly produced by Trinity were conducted using the DeCypher Tera-BLASTP algorithm on the TimeLogic DeCypher server located at Mount Desert Biological Laboratory (Salisbury Cove, ME, USA)."
Transcriptome analysis based on next-generation sequencing of non-model plants producing specialized metabolites of biotechnological interest.
"TimeLogic Decypher Biocomputing systems (http://www.timelogic.com) were used to significantly accelerate similarity searches. Specifically, the TimeLogic Tera-BLAST algorithm was used to compare transcripts to the NCBI databases NR(non-redundant) and the viridiplantae subset of RefSeq (Pruitt et al., 2007). An expected e-value of 1e-3 and a minimum alignment length of 30 bp were used. To obtain motif-level information, accelerated Hidden Markov Model (HMM) searches were performed against local instances of Interpro HMM libraries at an e-value of 1e-10."
Microbial Community Structure in a Seawater Flooding System in Saudi Arabia.
"The remaining high quality sequences were compared against the nonredundant SSU reference data set of SILVA102 using the Tera-BLAST algorithm on a TimeLogic decypher system from Active Motif, Inc., consisting of 12 boards. The Tera-BLAST results were used to screen for problematic, chimerical and eukaryotic sequences. Sequences having a best alignment covering less than 70% or having a best BLAST search hit an e-value greater than e-50 were excluded as problematic sequences."
Peptidergic signaling in Calanus finmarchicus (Crustacea, Copepoda): In silico identification of putative peptide hormones and their receptors using a de novo assembled transcriptome.
"Searches of the transcriptome assembly produced by Trinity were conducted using a DeCypher Tera-BLASTP algorithm on the Mount Desert Island Biological Laboratory's (Salisbury Cove, ME, USA) TimeLogic DeCypher server."
A novel metatranscriptomic approach to identify gene expression dynamics during extracellular electron transfer.
"The raw Illumina RNA sequence data files were converted from fastq to fasta format and then aligned against the SILVA (SSURef and LSURef) database, build 106 (April 2011), using tera-blastn on Decypher Timelogic hardware-accelerated boards. The best alignment against SILVA for each RNA sequence was extracted from the tera-blastn results."
Antennal transcriptome analysis of the chemosensory gene families in the tree killing bark beetles, Ips typographus and Dendroctonus ponderosae (Coleoptera: Curculionidae: Scolytinae).
"The 454 reads were assembled using Seqman Ngen to generate a backbone; subsequently, the Illumina reads were mapped onto this backbone using Seqman Ngen to correct for technology-inherent read errors. The resultant contigs were annotated using a Codequest Workstation (Timelogic/Active Motif, Carlsbad, CA)."
Pyrosequencing of the adult tarnished plant bug, Lygus lineolaris, and characterization of messages important in metabolism and development.
Entomologia Experimentalis et Applicata 146(3):364–378, March 2013.
"Assembled contiguous sequences, herein referred to as contigs, were initially identified using the Tera-BLASTX algorithm with DeCypher (TimeLogic) against Genbank non-redundant (nr) and expressed sequence tag (est) databases (downloaded June 2008)."
Characterization of transcriptomes from sexual and asexual lineages of a New Zealand snail (Potamopyrgus antipodarum).
Molecular Ecology Resources 13(2):289-294, March 2013.
"These searches were carried out at the University of Iowa using the Tera-BLASTX implementation of the BLASTX algorithm on a TimeLogic DeCypher system (Active Motif Inc., Carlsbad, CA) using default BLASTX parameters with default e-value or maximum-hit cutoffs."
"The annotation of tree leaves was performed using TimeLogic™ TERA-BLAST of OTU representative sequences against the November 2011 release of the NCBI nt database."
"All predicted gene models were functionally annotated using SignalP, TMHMM, InterProScan, BLASTp against GenBank nr, and hardware-accelerated double-affine Smith-Waterman alignments (deCypherSW; www.timelogic.com) against SwissProt (www.expasy.org/sprot), KEGG, and KOG.."
Oomycete transcriptomics database: A resource for oomycete transcriptomes.
"The primary annotation of the sequences was done with tera-BLASTX against a non-redundant protein database accelerated on the TimeLogic's DeCypher system."
"Functional annotation by similarity to genes from the GenBank non-redundant set using BLASTp alignments and hardware-accelerated double-affine Smith-Waterman alignments (http://www.timelogic.com) against SwissProt (http://www.expasy.org/sprot), the Kyoto Encyclopedia of Genes and Genomes (KEGG), and eukaryotic orthologous groups of proteins (KOG)."
In silico characterization of the insect diapause-associated protein couch potato (CPO) in Calanus finmarchicus (Crustacea: Copepoda).
Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, 8(1):45-57, March 2013.
"Searches of the contigs assembled from 454 pyrosequencing data were conducted using the DeCypher Tera-BLASTP algorithm on the Mount Desert Island Biological Laboratory's TimeLogic DeCypher server."
Detection of Multi-clustered Genes and Community Structure for the Plant Pathogenic Fungus Fusarium graminearum.
Computational Methods in Systems Biology: Lecture Notes in Computer Science, 2012, 69-86.
"The sequence similarity network was constructed from all-versus-all sequence matching of the proteins in version 3.2 of the Fusarium graminearum annotation (at ftp://ftpmips.gsf.de/FGDB/v32) implemented on a TimeLogic® Tera-BLAST™ (Active Motif Inc., Carlsbad, CA) system."
The LO-BaFL method and ALS microarray expression analysis.
"Re-map the Agilent probes to build 36.1 of the human genome using the accelerated Tera-BLAST algorithm, as implemented on a TimeLogic-Decypher server."
"Predicted gene models were functionally annotated using [...] hardware-accelerated double-affine Smith-Waterman alignments against KEGG and KOG."
Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche.
"All predicted gene models were functionally annotated using SignalP, TMHMM, InterProScan, BLASTp against GenBank’s database of non-redundant proteins, and hardware-accelerated double-affine Smith-Waterman alignments (deCypherSW) against SwissProt, KEGG, and KOG."
Molecular Plant-Microbe Interactions, 25(10):1350-1360. October 2012.
"All predicted gene models were functionally annotated by the JGI Annotation Pipeline using InterProScan (Zdobnov and Apweiler 2001) and hardware-accelerated double-affine Smith-Waterman alignments (http://www.timelogic.com/) against highly curated databases such as SwissProt (Bairoch et al. 2005), KEGG (Ogata et al. 1999), and Pfam (Bateman et al. 2004)."
Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, 7(2):110-123. June 2012.
"After clustering sequences, singletons and contigs were annotated again using BLASTx (Altschul et al., 1994), which was processed through a local (Mount Desert Island Biological Laboratory) TimeLogic DeCypher server (Active Motif, Inc); the ten top BLASTx hits were checked manually for consistency in annotation and degree of identity/similarity to the respective C. finmarchicus sequence."
Olson, Å., Aerts, A., Asiegbu, F., Belbahri, L., Bouzid, O., Broberg, A., Canbäck, B., Coutinho, P. M., Cullen, D., Dalman, K., Deflorio, G., van Diepen, L. T., Dunand, C., Duplessis, S., Durling, M., Gonthier, P., Grimwood, J., Fossdal, C. G., Hansson, D., Henrissat, B., Hietala, A., Himmelstrand, K., Hoffmeister, D., Högberg, N., James, T. Y., Karlsson, M., Kohler, A., Kües, U., Lee, Y.-H., Lin, Y.-C., Lind, M., Lindquist, E., Lombard, V., Lucas, S., Lundén, K., Morin, E., Murat, C., Park, J., Raffaello, T., Rouzé, P., Salamov, A., Schmutz, J., Solheim, H., Ståhlberg, J., Vélëz, H., de Vries, R. P., Wiebenga, A., Woodward, S., Yakovlev, I., Garbelotto, M., Martin, F., Grigoriev, I. V. and Stenlid, J.
New Phytologist, 194(4):1001-1013. June 2012.
"All predicted gene models were functionally annotated using [...] hardware-accelerated double-affine Smith–Waterman alignments (DeCypherSW; http://www.timelogic.com/decypher_sw.html) against SwissProt (http://www.expasy.org/sprot/), KEGG (Kanehisa et al., 2008) and KOG (Koonin et al., 2004)."
Proc Natl Acad Sci U S A. 2012 May 22; 109(21): E1377–E1386. Published online 2012 May 3. doi: 10.1073/pnas.1115433109 PMCID: PMC3361419.
"Sequence Processing and Annotation: The 47,343 initial 454 sequencing reads were processed and analyzed using a custom semiautomated processing pipeline first described in ref. 6. Briefly, Fasta-formatted sequences from 454 runs were assigned to libraries allowing one mismatch in the 10-bp barcode. All raw sequences were scanned for inverted repeat/direct repeat (IRDR) and linker recognition sequences using EMBOSS Vectorstrip with successively less stringent parameters (10%, 15%, and finally 20% mismatches allowed) until the maximum number of constructs (i.e., IRDR: GTGTATGTAAACTTCCGACTTCAACTG and linker sequence: GTCCCTTAAGCGGAGCCCT) were recognized and trimmed off. Only 44,294 sequences that had a matched IRDR with an insert sequence of at least 16 bp were carried further for mapping to the mouse genome. These trimmed insert sequences were mapped to the mouse genome (National Center for Biotechnology Information build 37) using BLASTN (DeCypher's TeraBLASTN; Active Motif), requiring query sequences to align within 1 bp of the end of the LTR sequence that was trimmed. Additionally, the query sequence was required to match with at least 95% identity. Ambiguous sequences that mapped to multiple genomic loci were removed, leaving 2,090 uniquely mappable nonredundant insertions. Unambiguously mapped nonredundant insertions were assigned to clusters of CISs if the local density of insertions in a given window size exceeded the density that would be expected by chance, as determined by Monte Carlo simulation. A CIS is defined as statistically significant if a region in the genome has three or more SB insertions with a 30-kb window or four or more insertions within 155 kb. CISs that occurred at the same nucleotide in different tumors from the same mouse were removed with the exceptions of Zfp608 and Bcl9. Nonredundant insertion positions were annotated using the EnsEMBL API with the name of the gene whose start site was closest to the position. CIS positions were annotated similarly using the median insertion position within the CIS as a reference point."
International Journal of Food Microbiology, online 14 May 2012.
"... and hardware-accelerated double-affine Smith–Waterman alignments (DeCypherSW; http://www.timelogic.com/decypher_sw.html) against SwissProt (http://www.expasy.org/sprot/), KEGG (Kanehisa et al., 2008) and KOG (Koonin et al., 2004)."
Developmental & Comparative Immunology, 36(4):665-679. April 2012.
"To enable the design of specific primers we used individual domains from nurse shark Igs to search the spiny dogfish EST database using the Tera-BLASTP protein to DNA search function and EST dogfish multi-tissue database."
PNAS, online 20 March 2012.
"All predicted gene models were functionally annotated using SignalP, TMHMM, InterProScan, BLASTp against NR, and hardware-accelerated double-affine Smith-Waterman alignments (DeCypherSW; http://www.timelogic.com/decypher_sw.html) against SwissProt (http://www.expasy.org/sprot/), KEGG and KOG."
FEMS Microbiology Ecology, online 14 March 2012.
"GOS metagenomes were queried by hidden Markov models (HMMs) belonging to these SCDs present in the Pfam 23.0 database (Finn, et al., 2008) using a single TimeLogic DeCypher card (Active Motif, Inc., Carlsbad, CA), and hits with E-values below 10 -10 were used for the standardization."
Environmental Microbiology, 14(3):754-764. March 2012.
"... using the Tera-Blast algorithm on a 16 board TimeLogic Decypher system (Active Motif, Inc.)."
Fungal Genetics and Biology. 49(3):217-226. March 2012.
"All predicted gene models were functionally annotated using SignalP (Nielsen et al., 1997), TMHMM (Melen et al., 2003), InterProScan (Zdobnov and Apweiler, 2001), BLASTp (Altschul et al., 1990) against nr, and hardware-accelerated double-affine Smith-Waterman alignments (DeCypherSW; http://www.timelogic.com/decypher_sw.html) against SwissProt (http://www.expasy.org/sprot/), KEGG (Kanehisa et al., 2008), and KOG (Koonin et al., 2004)."
"The remaining high-quality sequences were compared against the non-redundant SSURef data set of SILVA102 (Pruesse et al. 2007) using the Tera-Blast algorithm on a 16-board TimeLogic Decypher system (Active Motif, Inc.)."
"The BESs were then compared against the human reference genome NCBI build 36.1 (not including alternate assemblies), and also against db 'NT' (the nucleotide sequence collection; ftp://ftp.ncbi.nih.gov/blast/db/FASTA/nt.gz) using the Tera-BLASTN algorithm (TimeLogic Biocomputing Solutions) with a cutoff of e-50 for the matches to the human reference genome, and only BESs with a primary hit to the human reference sequence meeting the e-50 cutoff and a next best hit with a score of e-10 or greater were included in the virtual map."
FEMS Microbiology Ecology. 79(1):240-250. January 2012.
"The remaining high-quality sequences were compared against the nonredundant SSU Ref data set of silva102 (Pruesse et al., 2007) using the Tera-blast algorithm on a TimeLogic Decypher system (Active Motif, Inc.) consisting of 12 boards. Tera-blast results were used to screen for problematic, chimeric, and eukaryotic sequences."
"A best gene match between genes in O. tauri and O. lucimarinus and genes in the union of KEGG plant genomes (meta-plant) was found using the Smith-Waterman algorithm (Smith et al., 1981) performed on a TimeLogic DeCypher (Active Motif Inc., Carlsbad, CA) gene comparison server."
BMC Genomics 2011, 12:557, online November 14, 2011.
"The sequenced animal was genotyped with BovineHD and BovineSNP50 BeadChips (Illumina, San Diego, California, USA). To accurately detect chromosomal positions of the SNP sites, Tera-Blast (Timelogic, USA) was used for mapping the flanking SNP sequences against both the UMD3.1 and Btau4.0 genome assemblies."
Transcript profiling reveals expression differences in wild-type and glabrous soybean lines.
BMC Plant Biology 2011, 11:145. doi:10.1186/1471-2229-11-145. Published: 26 October 2011.
"...the 78,744 models (that include both high and low confidence models) were further annotated using BLASTX against the non-redundant (nr) database of the National Center for Biotechnology Information and trEMBL and Swiss prot of the European Bioinformatics Institute on a Time Logic CodeQuest DeCypher Engine."
Nature Biotechnology 29:922–927, online October 2, 2011.
"All predicted gene models were functionally annotated using SignalP, TMHMM, InterProScan, Blastp against the nr database, and hardware-accelerated double-affine Smith-Waterman alignments (DeCypherSW; http://www.timelogic.com)"
BMC Genomics 2011, 12:488, October 6, 2011.
"The annotation of the respective contigs included in the microarray, based on a Carcinus maneas EST library (deposited at http://www.ncbi.nlm.nih.gov), was performed by Towle et al. using BLASTX analysis on a local TimeLogic DeCypher server (Active Motif, Inc.)."
Applied and Environmental Microbiology, 77(19):6908-6917, October 2011.
"The remaining high quality sequences were compared against the non-redundant SSU_Reference data set SILVA102 using the Tera-Blast algorithm on a 16 board TimeLogic Decypher system (Active Motif, Inc.)."
Genetics, September 1, 2011; 189(1):55-69.
"All predicted gene models were functionally annotated using SignalP (Nielsen et al. 1997); TMHMM (Melen et al. 2003); InterProScan (Zdobnov and Apweiler 2001); BLASTp (Altschul et al. 1990) against nr; and hardware-accelerated double-affine Smith–Waterman alignments (deCypherSW; http://www.timelogic.com/catalog/758/decyphersw) against SwissProt (Boeckmann et al. 2003), KEGG (Kanehisa et al. 2008), and KOG (Koonin et al. 2004)."
Insect Molecular Biology, 20(4):465–491, August 2011.
"... assembly of GS-FLX sequencing reads was carried out with the GS Assembler ver. 1.1.02.15 (Roche) using default parameters. Assembled contiguous sequences, herein referred to as contigs, were initially identified using the Tera-BLASTX algorithm with DeCypher (TimeLogic) against local custom databases consisting of the GenBank nr and EST databases (downloaded June 2008)."
"Removal of primer sequence contamination and assembly of GS-FLX sequencing reads was carried out with the GS Assembler ver. 1.1.02.15 (Roche) using default parameters. Assembled contiguous sequences, herein referred to as contigs, were initially identified using the Tera-BLASTX algorithm with DeCypher (TimeLogic) against local custom databases consisting of the GenBank nr and EST databases (downloaded June 2008)."
Applied Microbiology and Biotechnology 91(3):799-810, August 2011.
"... using the Tera-BLAST algorithm on a TimeLogic Decypher system (Active Motif, Inc.) consisting of 12 boards."
PLoS ONE 6(8):e22870. August 12, 2011.
"Prediction of microRNA candidates was performed using the miRDeep miRNA prediction program... The miRDeep code was modified [...] to utilize Decypher Timelogic hardware accelerated boards for the alignment."
Systematic and Applied Microbiology, In Press (Available online 14 June 2011).
"Unaligned 23S/28S rRNA fragments retrieved by the SILVA pipeline were used to query the reference dataset of SILVA LSU release 102, using the Tera-BLASTN algorithm (Tera-BLAST™, TimeLogic Inc., Carlsbad, CA, USA)."
Vanden Wymelenberg A, Gaskell J, Mozuch M, Splinter Bondurant S, Sabat G, Ralph J, Skyba O, Mansfield SD, Blanchette RA, Grigoriev IV, Kersten PJ, Cullen D.
Appl Environ Microbiol. 2011 Jul;77(13):4499-4507.
"To identify P. chrysosporium homologs, the 12,438 P. placenta protein models represented on microarrays were aligned with all 10,048 v2 P. chrysosporium protein models by using Timelogic (Active Motif, Carlsbad, CA) hardware accelerated double-affinity Smith-Waterman alignments..."
"Sequence analysis: We constructed profile HMMs for the ePK, PIKK, RIO, ABC1, PDK, and alpha-kinase families with HMMer and used these to search the ORF, genomic, and EST sequences using Decypher hardware-accelerated HMMer implementation from Time Logic (Carlsbad, CA, USA)."
Andersen MR, Salazar MP, Schaap PJ, van de Vondervoort PJ, Culley D, Thykaer J, Frisvad JC, Nielsen KF, Albang R, Albermann K, Berka RM, Braus GH, Braus-Stromeyer SA, Corrochano LM, Dai Z, van Dijck PW, Hofmann G, Lasure LL, Magnuson JK, Menke H, Meijer M, Meijer SL, Nielsen JB, Nielsen ML, van Ooyen AJ, Pel HJ, Poulsen L, Samson RA, Stam H, Tsang A, van den Brink JM, Atkins A, Aerts A, Shapiro H, Pangilinan J, Salamov A, Lou Y, Lindquist E, Lucas S, Grimwood J, Grigoriev IV, Kubicek CP, Martinez D, van Peij NN, Roubos JA, Nielsen J, Baker SE.
"All predicted gene models were functionally annotated by sequence similarity to annotated genes from the NCBI nonredundant set and other specialized databases (such as KEGG) (Kanehisa et al. 2002, 2004) using BLAST and hardware accelerated double-affine Smith-Waterman alignments (http://www.timelogic.com)."
Stephen B. Goodwin, Sarrah Ben M'Barek, Braham Dhillon, Alexander H. J. Wittenberg, Charles F. Crane, James K. Hane, Andrew J. Foster, Theo A. J. Van der Lee, Jane Grimwood, Andrea Aerts, John Antoniw, Andy Bailey, Burt Bluhm, Judith Bowler, Jim Bristow, Ate van der Burgt, Blondy Canto-Canché, Alice C. L. Churchill, Laura Conde-Ferràez, Hans J. Cools, Pedro M. Coutinho, Michael Csukai, Paramvir Dehal, Pierre De Wit, Bruno Donzelli, Henri C. van de Geest, Roeland C. H. J. van Ham, Kim E. Hammond-Kosack, Bernard Henrissat, Andrzej Kilian, Adilson K. Kobayashi, Edda Koopmann, Yiannis Kourmpetis, Arnold Kuzniar, Erika Lindquist, Vincent Lombard, Chris Maliepaard, Natalia Martins, Rahim Mehrabi, Jan P. H. Nap, Alisa Ponomarenko, Jason J. Rudd, Asaf Salamov, Jeremy Schmutz, Henk J. Schouten, Harris Shapiro, Ioannis Stergiopoulos, Stefano F. F. Torriani, Hank Tu, Ronald P. de Vries, Cees Waalwijk, Sarah B. Ware, Ad Wiebenga, Lute-Harm Zwiers, Richard P. Oliver, Igor V. Grigoriev, Gert H. J. Kema.
"All predicted gene models were annotated using InterProScan and hardware-accelerated double-affine Smith-Waterman alignments (www.timelogic.com) against the SwissProt (www.expasy.org/sprot) and other specialized databases such as KEGG."
Richard L Tillett, Ali Ergül, Rebecca L Albion, Karen A Schlauch, Grant R Cramer and John C Cushman.
BMC Plant Biology 2011, 11:86.
"Database searches using the BLAST were performed using the Tera-BLAST™P algorithm, open penalty 11, extend penalty 1, double-affine Smith-Waterman window 50, and maximum e-value cutoff 1 × 10-3 on TimeLogic DeCypher hardware (Active Motif, Inc., Carlsbad, CA)."
The ISME Journal (2011) 5, 107–121.
"Specialized tblastn (BLOSUM62 substitution matrix) of predicted Phage H105/1 proteins and of nine other marine phages was carried out against all six reading frames of virome nucleotide reads using DeCypher hardware (TimeLogic, Inc., Carlsbad, CA, USA)."
Comparative Biochemistry and Physiology Part D: Genomics and Proteomics (2011) 6(2):115-125.
"The total of 4,483 putatively unique contigs were submitted to BLASTX analysis on a local TimeLogic DeCypher server (Active Motif, Inc.) to authenticate the constituent EST results and to assist in annotating the resulting microarray."
Assessing the functional coherence of modules found in multiple-evidence networks from Arabidopsis.
"Sequence similarity was determined by using TimeLogic® Tera-BLAST™ (Active Motif Inc., Carlsbad, CA) for all-against-all sequence-comparison of proteins in the interaction dataset."
Niche of harmful alga Aureococcus anophagefferens revealed through ecogenomics.
"All predicted gene models were annotated using InterProScan and hardware-accelerated double-affine Smith-Waterman alignments (www.timelogic.com) against SwissProt (www.expasy.org/sprot) and other specialized databases like KEGG. [...] Pfam domains were identified using TimeLogic implementation of HMMER package."
Microbially Influenced Corrosion In Oil Sands Water Handling Facilities.
CORROSION 2011, March 13 - 17, 2011 , Houston, Texas.
"... High quality sequences were compared against the non-redundant small subunit (SSU) ribosomal RNA database (SILVA102)11 using the Tera-BLAST (Basic Local Alignment Search Tool) algorithm on a TimeLogic Decypher system (Active Motif, Inc.)."
Human Mutation 32(2):E1999–E2017, February 2011.
"To verify the sequencing process quality, the original 454 reads were queried (Tera-BLASTN, Decypher v7.6.2.1) against a custom database of contaminating sequences."
We also used SSR primer sequences (~20 bp in length) in pairs directly as query sequences to search for homologies against the A. thaliana pseudochromosomes, using the Tera-Probe algorithm with both gapped alignment and query filter options off."
Carbon and sulfur cycling by microbial communities in a gypsum-treated oil sands tailings pond.
Ramos-Padrón E, Bordenave S, Lin S, Bhaskar IM, Dong X, Sensen CW, Fournier J, Voordouw G, Gieg LM.
Environ Sci Technol. 2011 Jan 15;45(2):439-46.
"... The remaining high quality sequences were compared against the nonredundant SSU ref data set of SILVA102 (24) using the Tera-BLAST algorithm on a TimeLogic Decypher system (Active Motif, Inc.) consisting of 12 boards."
Journal of Insect Physiology (2011) 57(1)52-61.
"Assembled contiguous sequences, referred to as contigs, were identified using the Tera-BLASTX algorithm with DeCypher (TimeLogic, Carlsbad, CA)."
Development and Application of Bovine and Porcine Oligonucleotide Arrays with Protein-Based Annotation.
John R. Garbe, Christine G. Elsik, Eric Antoniou, et al.
Journal of Biomedicine and Biotechnology, vol. 2010, Article ID 453638, 11 pages.
"Annotation of probes on both microarrays was reassessed to take advantage of the most recent builds of the bovine and porcine genomes. To assign annotation to the 23,580 bovine oligo probes the consensus sequences were compared to the UMD2.0 build of the bovine genome with GMAP and the Decypher system GeneDetective program resulting in alignment of 21,976 consensus sequences with coverage ≥50% and identity ≥95%. Of these, 20,336 have coverage ≥95%."
Expressed sequence tag (EST) profiling in hyper saline shocked Dunaliella salina reveals high expression of protein synthetic apparatus components.
Plant Science, Volume 179, Issue 5, November 2010, Pages 437-449.
"... Release 2010_06 of May 19, 2010) using Tera-BLASTP (double-banded Smith–Waterman), word size 3, gap open penalty = 11, extension penalty = 1, and a minimum significance of 1e-2 using DeCypher™ programmable logic hardware (TimeLogic, Inc., Carlsbad, CA) at ..."
An in silico study of the genes for the isoflavonoid pathway enzymes in soybean reveals novel expressed homologues.
Canadian Journal of Plant Science, 2010, 90:453-469.
"All clustered EST consensus sequences were mapped to the genome sequences using standalone BLASTN (Altschul et al. 1990) installed on a TimeLogic CodeQuest DeCypher Engine, in order to see the results unmasked."
Applying graph theoretic approaches to microbial metagenomes: ecological perspectives on function.
Wolfgang Hankeln, Pier Luigi Buttigieg, Ivaylo Kostadinov, Renzo Kottmann, Pelin Yilmaz, Melissa Beth Duhaime, and Frank Oliver Glöckner.
In Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology (BCB '10) (2010). ACM, New York, NY, USA, 478-480.
"... GS148-GS 149, and MOVE858 were downloaded from the CAMERA web portal and queried by all hidden Markov models (HMMs) belonging to protein domains of unknown function present in the PFAM 23.0, pfam_fs database using a single TimeLogic DeCypher card ..."
"TimeLogic's DeCypher system (available from Active Motif, Inc.) offers a hardware-accelerated implementation of the BLAST algorithm (TeraBLAST™). MULTBLAST utilizes these accelerated searches, thus allowing the completion of a large number of BLAST searches against large databases within a reasonable amount of time."
PLoS ONE (2010), 5(9): e12812.
To enrich annotation of the probes and probe-sets, A. thaliana homologues were derived from the highest scoring alignment to A. thaliana coding sequences (TAIR v9) using the TimeLogic® Tera-BlastN™ algorithm (Active Motif Inc.)."
MicroRNA identity and abundance in porcine skeletal muscles determined by deep sequencing.
Animal Genetics. Volume 41, Issue 2, pages 159–168, April 2010.
"The mirbase version 12.0 containing the mature miRNAs (http://microrna.sanger.ac.uk/ sequences) was downloaded and a blastn search with the unique sequence reads was performed using the Tera-BLASTN algorithm on a DeCypher FPGA computer."
The Genome of Naegleria gruberi Illuminates Early Eukaryotic Versatility.
"Protein function predictions were made for all predicted gene models using the following collection of software tools: SignalP (http://www.cbs.dtu.dk/services/SignalP/), TMHMM (http://www.cbs.dtu.dk/services/TMHMM/), InterProScan (http://www.ebi.ac.uk/interpro/; Quevillon et al., 2005), and hardware-accelerated double-affine Smith-Waterman alignments (http://www.timelogic.com/decypher_sw.html) against SwissProt (http://www.expasy.org/sprot/), KEGG (http://www.genome.jp/kegg/), and KOG (http://www.ncbi.nlm.nih.gov/COG/)."
Insect Biochemistry and Molecular Biology (2010) 40(1):79-90.
"Assembled contiguous sequences, herein referred to as contigs, were initially identified using the Tera-BLASTX algorithm with DeCypher (TimeLogic) against Genbank nr."
Seed storage protein gene promoters contain conserved DNA motifs in Brassicaceae, Fabaceae and Poaceae.
BMC Plant Biology 2009, 9:126.
"Smith-Waterman alignments of the soybean predicted peptides corresponding to the top-ten scoring promoters was performed against the Uniprot release 14.6 (plant sequences) using a TimeLogic DeCypher system."
Male engorgement factor: Role in stimulating engorgement to repletion in the ixodid tick, Dermacentor variabilis.
Donohue KV, Khalil SM, Ross E, Mitchell RD, Roe RM, Sonenshine DE.
J Insect Physiol. 2009 Oct;55(10):909-18.
"Assembled contiguous sequences, herein referred to as contigs, were initially identified using the Tera-BLASTX algorithm with DeCypher (TimeLogic) against GenBank nr and ..."
MATE Transporters Facilitate Vacuolar Uptake of Epicatechin 3'-O-Glucoside for Proanthocyanidin Biosynthesis in Medicago truncatula and Arabidopsis.
The Plant Cell 21:2323-2340 (2009).
"The gene encoding this protein could be critical for engineering PA accumulation in forage legumes. No candidate gene was represented on the Medicago Affymetrix array previously used to study the Arabidopsis TT2-induced Medicago hairy root transcriptome (Pang et al., 2008Go). We therefore mined for Medicago MATE sequences using the Arabidopsis TT12 protein sequence to BLAST against the M. truncatula annotated genome protein database [using TimeLogic's accelerated DeCypher Tera-BLASTP algorithm]."
Molecular Analysis of Persistent Periradicular Lesions and Root Ends Reveals a Diverse Microbial Profile.
Journal of Endodontics 35(7):950-957, July 2009.
"The sequences generated were compared with the GenBank database to identify the closest match using a Time Logic DeCypher TeraBlast server hosted by the Ohio Supercomputer Center (Columbus, OH)."
Transcriptome sequencing of the Microarray Quality Control (MAQC) RNA reference samples using next generation sequencing.
"mapping of all of the 3.6 million reads in this study could be mapped to either the much larger AceView database in an overnight run or to the entire human genome in 6 days using the TimeLogic DeCypher accelerator board."
The Cell Cycle Ontology: an application ontology for the representation and integrated analysis of the cell cycle process.
"The input all-against-all BLAST matrix for the four complete proteomes is produced with the Tera-BLAST hardware implementation of BLAST with default parameter settings."
GarlicESTdb: an online database and mining tool for garlic EST sequences.
BMC Plant Biology 2009, 9:61.
"After the pre-processing step finished making EST consensus sequences, we assigned putative functions to the garlic ESTs based on BLASTN (Query Coverage ≥ 80.0%, Identity ≥ 70.0%, E-value ≤ 1.0E-20), BLASTX and TBLASTX (Match No. ≥ 50 aa, Identity ≥ 25.0%, E-value ≤ 1.0E-20) searches against the GenBank NT and NR databases (ftp://ftp.ncbi.nih.gov/blast/db/FASTA/) using a TimeLogic DeCypher system (Active Motif, Inc.)"
Amphioxus encodes the largest known family of green fluorescent proteins, which have diversified into distinct functional classes.
BMC Evolutionary Biology 2009, 9:77.
"Searches for GFPs in other sequence sources used Blast, Psi-Blast, HMMer and Gene Detective, a hardware implementation of the Genewise algorithm (Active Motif, Carlsbad, CA)."
BC10, a DUF266-containing and Golgi-located type II membrane protein, is required for cell-wall biosynthesis in rice (Oryza sativa L.).
The Plant Journal, Volume 57, Issue 3, pages 446–462, February 2009.
"Systematic identification of DUF266-containing proteins in the NCBI nr databases was performed using a TimeLogic implemented profile search engine with default parameters through a CodeQuest work station."
Nucl. Acids Res. (2009) 37 (2): 550-556.
"An all-versus-all search of the elk dataset using four TimeLogic DeCypher boards (http://www.timelogic.com) all patterns occurring for a minimum of 20 × (based on the number of infected animals), with none of the top 100 BLAST (13) matches occurring in non-target samples, yielded 10 634 motifs specific to control and infected animals up to 5 months after infection; and 4933 motifs for animals at least 8 months after infection (motifs of 35 bases or less, using a sliding window for longer matches)."
"GS FLX data processing was performed using the Roche GS FLX software (Release: 1.1.03.24). Base-called reads were trimmed and filtered for quality and converted into FASTA format. A total of 666,864 and 95,222 quality filtered reads obtained from the MS and NVS libraries respectively were further processed in the KeyPoint pre-processing step. During pre-processing, the origin of the reads was identified based on the target-specific primer sequences and the six base sample identification tags.
This step was implemented in a custom Perl script that used the Semi Global Smith Waterman algorithm within a TimeLogic DeCypher system (Active Motif, Inc.)."
"Annotation of the SNP-containing genes. Sequences surrounding the SNPs were subjected to blast analysis on a DeCypher FPGA computer using the accelerated BLASTNH algorithm (Timelogic/Active Motif)."
"Subsequently, we used Tera-Probe™ an algorithm similar to the BLAST sequence search algorithm but optimized for small oligonucleotide sequences. Tera-Probe™ was used to query the probes within the CNVRs against the newest available version of the Sus Scrofa assembly..."
"The Tera-BLAST™N sequence similarity algorithm was used to query the CNVR sequences against the pig Unigene and the Refseq vertebrate mammalian mRNA databases."
"...the “TimeLogic” (http://www.timelogic.com) implementation of HMMER was used because it has a higher throughput and sensitivity compared to the BLAST approach."
"5,484 ESTs (Expressed Sequence Tags) and 4,242 gDNAs of N. ovalis were sequenced. Vectors and linkers were automatically filtered out of sequences. First the vector pieces were detected using a BlastN search against their respective vector sequences on a TimeLogic DeCypher..."
"...All sequence comparisons were run on a DeCypher TimeLogic using the Smith-Waterman algorithm for pairwise sequence comparisons and Hidden Markov Models for sequence-to-profile comparisons, active motifs included. The output was subsequently analyzed in a Linux environment using Perl scripts."
Nucleic Acids Res., Dec 2008; 37(2):550-556.
"...An all-versus-all search of the elk dataset using four TimeLogic DeCypher boards (http://www.timelogic.com) all patterns occurring for a minimum of 20 x (based on the number of infected animals), with none of the top 100 BLAST (13) matches occurring in non-target samples, yielded 10 634 motifs specific to control and infected animals up to 5 months after infection; and 4933 motifs for animals at least 8 months after infection (motifs of 35 bases or less, using a sliding window for longer matches)..."
"...The resulting sequences were then compared against the GenBank non-redundant database using the BLASTX algorithm. Batch blasts were performed using the CodeQuest system..."
"...TIGR, and in-house HMM ( SI Text, Figs. S3 and S4 ) with Global and Glocal models were performed with a hardware-accelerated DeCypher system (Active Motif). E value cutoffs of e = 10 were used to pick up repeated elements whose individual scores were very low..."
Journal of Orthopaedic Research, June 2008, 26(6):764–771.
"The names and functions of genes were annotated by the commercially available software (BlastN, TimeLogic Corp, Carlsbad, CA"
"To identify segments of the E. faecalis V583 genome that are absent from the genome of strain OG1RF, the partially assembled OG1RF contigs were obtained from the Baylor College of Medicine website. The nucleotide sequences of all annotated V583 open reading frames (ORFs) (obtained from TIGR) were compared with the OG1RF contigs using the Smith-Waterman algorithm computed with the TimeLogic DeCypher software program (Active Motif, Inc.). The top-ranked hit for each V583 ORF was examined for percent alignment with the OG1RF contig. Hits with greater than 90% alignment were considered matches and scored as present in the OG1RF genome. Tabulation of the results on an ORF-by-ORF basis revealed the presence of multigene gaps missing from the OG1RF genome, some of which were previously known."
"...order to demonstrate the proposed approach, a prediction web server, as well as a command line interface, was implemented. The Decypher hardware system, provided by Active Motif Incorporation, was utilized to conduct the BLAST search and multiple CPU/computers..."
"...implemented at the Boyce Thompson Institute. Arabidopsis (version...domain database (Bateman et al. 2004) with a TimeLogic Decypher system ( http://codequest.bti.cornell.edu/chlre ). The same sequences..."
"...We also used tBLASTx to search against the Human (Hs) Unigene database (Build 201), the NCBI Chicken protein database (downloaded May 17, 2007) and the Chicken International Protein Index (IPI, Release 3.26). Default parameters were used for all BLASTs, which were performed locally with TimeLogic Server..."
J. Exp. Bot., Mar 2008; 59(7):1875-1894.
"...word size 3, gap open penalty=11, extension penalty=1, and a minimum significance of 1e5 using DeCypher programmable logic hardware (TimeLogic, Inc., Carlsbad, CA, USA) at the Nevada Center for Bioinformatics. Functional categories were assigned..."
"In order to demonstrate the proposed approach, a prediction web server, as well as a command line interface, was implemented. The DeCypher hardware system, provided by Active Motif Incorporation, was utilized to conduct the BLAST search and multiple CPU/computers were run in parallel to perform HMM modeling and scoring."
"The protein sequences of the microsporidium Encephalitozoon cuniculi and of 25 fungi ... were downloaded rom the corresponding sequencing projects. Similarity scores between the proteomes were computed using the Smith–Waterman P algorithm (Smith & Waterman 1981) on a TimeLogic DeCypher (matrix: Blosum62; e-value cut-off: 0.01; low-complexity filter on). The orthologous groups were constructed by an approach similar to that used for the COGs (Tatusov et al. 2000)."
J Am Chem Soc. 2008 January 9; 130(1):176–185.
"All secondary structural elements in the shuffling pool were selected from unique E. coli proteins with structures on file in the Protein Data Bank (PDB). PDB files of these proteins were submitted to the program PROMOTIF and the output files annotating the elements of secondary structure and the primary sequence of each element, as well as loop primary sequence data from the Sloop database, were submitted to DeCypher FrameSearch BLAST (Active Motif, Inc.) to obtain the E. coli nucleotide sequences encoding each element."
"...The final step in the mRNA target prediction process examined the mRNA targets for conservation in C. savignyi. Currently, predicted transcripts of C. savignyi do not exist. C.savignyi "pseudo" mRNAs were generated as follows. The tera-tblastn program on the TimeLogic board aligned the C.intestinalis mRNA gene sequences against the entire C. savignyi genome. The top match of the C. savignyi genome to each of the mRNA sequences was classified as an orthologous C. savignyi mRNA. The target prediction code was applied to the C. savignyi subsequences, to check that miRNAs matched the 3'UTR of orthologous genes to C. intestinalis, according to the seed match criteria described earlier..."
"...EST clusters for human gene transcripts in NCBI's RefSeq database release 17  were created using BLASTN sequence similarity program implemented to run on a DeCypher computer [http://www.timelogic.com] with P-value at or below 10−8..."
"...The identification of exonic fragments was carried out using TimeLogic® GeneDetective™ (Active Motif Inc., Carlsbad, CA) In order to directly relate the exons to the associated BES fragments and to accommodate the processing restrictions of Gene Detective, the identical 36 Mbp single sequence used for sequence comparison was divided into smaller, 999 bp linear order fragments, then tested these against the non-redundant fungal EST database (downloaded from NCBI on Nov 16, 2006; 886,100 fungal ESTs). We used only the top two ranked hits for each sequence and removed overlapping results..."
"...The PFAM alignments were downloaded from http://pfam.wustl.edu/hmmsearch.shtml and the HMMr searches were run locally on a Timelogic computer..."
"...Novel kinases were identified from the Celera human genomic sequence databases, and from the public Human Genome Sequencing project (http://www.ncbi.nlm.nih.gov/) using a hidden Markov model (HMMR) built with 70 mammalian and yeast kinase catalytic domain sequences. These sequences were chosen from a comprehensive collection of kinases such that no two sequences had more than 50% sequence identity. The genomic database entries were translated in six open reading frames and searched against the model using a Timelogic Decypher box with a Field programmable array (FPGA) accelerated version of HMMR2.1..."
"...Domains present in EDR2 were identified with the Hidden Markov Model program... [59. Stanford TimeLogic Hidden Markov Model Software]..."
"...We first performed all-against-all double affine Smith-Waterman alignments of the peptides in X. laevis and X. tropicalis using a TimeLogic DeCypher system (Active Motif, Inc., 1914 Palomar Oaks Way, Suite 150, Carlsbad, CA. 92008) with BLOSUM62 scoring matrix, gap opening penalty -15, gap extension penalty -2 until gap size 10, with no additional extension penalties. We identified the conserved four-fold degenerate amino acids within the alignments, extracted the corresponding codons in the underlying DNA sequence and calculated the 4 DTv distances (D4DTv) between each aligning pair as the fraction of four-fold degenerate (4D) third codon positions in which transversions are observed to have occurred. This provides a measure of the evolutionary distances between genes that is largely independent of the gene families, unlike measures based on peptides..."
"...The zebrafish doublets shown in Figure 1a were determined as follows: the Ensembl  models v. 24.4.1 were aligned to each other and to the Ensembl models v. 26.35.1 for human on Timelogic Decypher™ using the same parameter settings as for the frog aligments, and 4 DTv distances were determined for each pair with 25 or more 4D codon sites..."
"Global sequence similarity searches were performed using the amino acid sequences of all the conserved essential polynucleotide sequence against a non-redundant protein database using the Smith-Waterman algorithm with default parameters on a TimeLogic DeCypher system..."
"...sensitivity. EST clustering was performed using the accelerated BLAST (Altschul et al., 1997) based TeraClu algorithm on a DeCypher FPGA Computer (Timelogic/Acitve Motif) followed by cluster assembly using Phrap (Green,P., unpublished data). EST and contig.."
"...Predicted genes were annotated by using double-affine Smith-Waterman (TimeLogic) alignments against proteins from the National Center for Biotechnology In-formation nonredundant protein database, protein..."
Scalable Computing: Practice And Experience (2007) 8(2):167–171.
"First, coiled-coil sequences were masked by replacing amino acids predicted to be inside a coiled-coil region with the generic letter X. The masked sequence set was then compared in an all-against-all approach using the Smith-Waterman (SW Search) sequence comparison algorithm . Smith-Waterman analysis was accomplished with the TimeLogic De-Cypher system using the blossum62 scoring matrix."
"...Discovery and classification of kinase genes. Sequences used consisted of 17,422,766 open reading frames from GOS, 3,049,695 predicted open reading frames from prokaryotic genomes, and 2,317,995 protein sequences from NCBI-nr of February 10, 2005, as described . Profile HMM searches were performed with a Time Logic Decypher system (Active Motif) using in-house profiles for ePK, Haspin, Bub1, Bud32, Rio, ABC1 (UbiB), PI3K, and AlphaK domains, as well as Pfam profiles  for ChoK, APH, KdoK, and FruK, and TIGRFAM profiles  for HSK2 (thrB_alt), UbiB, and MTRK. A number (69) of additional ePK-annotated models from Superfamily 1.67  were used to capture initial hits but not for further classification. Initial hits were clustered and re-run against all models, and each model was rebuilt and rerun three to seven times using ClustalW , MUSCLE , and hmmalign (http://hmmer.janelia.org) to align, followed by manual adjustment of alignments using Clustal and Pfaat  and model building with hmmbuild. Low-scoring members of each family (e > 1 × 10−5) were used as seeds to build new putative families, and profile–profile and sequence–profile alignments were used to merge families into a minimal set (Dataset S2). A motif-based Markov chain Monte Carlo multiple alignment model  based on the conserved motifs of Figure 3 was run independently and used to verify HMM hits and seed new potential families for blast-based clustering, model building, and examination for conserved residues. Final family assignment was by scoring against the set of HMM models, with manual examination of sequences with borderline scores (e > 1 × 10−5 or difference in e-values between best two models >.01)..."
"...Searching sequences using profile HMMs. The full set of 7,868 Pfam release 17 models was used, along with additional nonredundant profiles from TIGRFAM (1,720 of 2,443 profiles; version 4.1). HMM profiling was carried out using a TimeLogic DeCypher system (Active Motif, Inc.) and took 327 hours in total (on an eight-card machine). A sequence was considered as matching a Pfam (fragment model) if its sequence score was above the TC score for that Pfam and had an E-value ≤ 1 × 10−3. It was considered as matching a TIGRFAM if the match had an E-value ≤ 1 × 10−7..."
"...PLAN integrates, by default, the Decypher hardware-based BLAST solution provided by Active Motif Inc. with a greatly improved efficiency over conventional BLAST software..."
"...BLAST searches were performed using either the DeCypher Tera-BLAST™ (Active Motif, Inc. Carlsbad, California, USA) or NCBI BLAST program..."
"...We used the Smith-Waterman implementation of the TimeLogic's DeCypher® accelerated hardware..."
Integr. Comp. Biol., Dec 2006; 46(6):912-918.
"All of the resulting contigs and singlets were submitted to blastx analysis using the Tera-BlastP algorithm (translated nucleotide sequence versus protein sequence) on a DeCypher server (TimeLogic), with reference to the non-redundant protein sequence database from NCBI. Positive hits with an E-value <0.0001 were obtained for 44.7% of the Carcinus contigs and 33.9% of the Homarus contigs, and for 47.4% of the Carcinus singlets and 39.3% of the Homarus singlets"
"Sequence similarity was detected by the Smith and Waterman method (Smith Waterman, 1981) on a DeCypher hardware-accelerated system (Active Motif, Carlsbad, CA)."
"...amplicon. The sequences generated were compared to the GenBank database to identify the closest match using a Time Logic DeCypher TeraBlast server hosted by the Ohio Supercomputer Center. Sequences with low homology to GenBank entries were screened for chimeras..."
"...BLAST comparisons of PDFs and POFs among different proteomes were performed using TeraBLAST running on an accelerated DeCypher server....'All-against-all' comparisons used to generate sets of species-specific proteins for both PDFs and POFs from Sc, Sp, At, Os, Dm, Ag, Ce, Mm, Rn and Hs were performed using TeraBLAST running on an accelerated DeCypher server , with a cutoff threshold of 10-6."
"...a DeCypher hardware-accelerated system (Active Motif) was used to perform HMMER searches against nucleic acid sequences."
"We searched the genomes for homologs using the Smith-WatermanP algorithm  on a TimeLogic DeCypher in all query-database combinations (matrix: Blosum62; e-value cutoff:100). In the case of spurious asymmetries in the similarity search (e.g. two sequences giving different alignments depending on which was the query), the results are the average of two values, including both reciprocal experiments..."
PNAS, Dec 2005; 102(4):17792-17797 and supporting information.
"Amino acids alignments were performed by using the ClustalW algorithm available from DeCypher..."
BMC Evol Biol. 2005; 5: 66. November 16 2005. doi: 10.1186/1471-2148-5-66.
"Smith-Waterman comparison was conducted using the TimeLogic Smith-Waterman implementation at OSC and the Blosum62 scoring matrix on all unique sequences in the combined sequences set. Sequences with masked coiled-coil domains were used as query on unmasked sequence sets as target. A P-score cut-off of 1.0e-03 was used as a threshold for selecting sequence similarity relationships. For sequences to be characterized as pair-wise similar and recovered for use in the clustering analysis, the P-score value must be less than this threshold based on the query-target Smith-Waterman comparison..."
Molecular Phylogenetics and Evolution, 36(3):536-545, September 2005.
"Gene-for-gene, pairwise comparisons were made between different species using the Hardware Accelerated, Tera-BLAST algorithm (Time-Logic, Crystal Bay, NV) executed on three TimeLogic DeCypher nodes."
J. Clin. Microbiol., Aug 2005; 43(8):3944-3955.
"The sequences generated were compared to the GenBank database to identify the closest relatives by using a Time Logic DeCypher Tera BLAST server hosted by the Ohio Supercomputer Center."
Protein Sci., Jun 2005; 14(6):1472-1484.
"A DeCypher hardware-accelerated bioinformatics system (TimeLogic, Inc.) was used to perform the Smith-Waterman, FrameSearch, and HMMER searches described below. The Smith-Waterman algorithm (Smith and Waterman 1981) was used to compare the amino acid sequence of CFE88 with protein sequences from completed microbial genomes, and the FrameSearch algorithm (Edelman et al. 1995) was used to compare CFE88 with nucleotide sequences from unfinished microbial genomes, using the DeCypher system as described in Healy (2003)."
Steven B. Cannon, John A. Crow, Michael L. Heuer, Xiaohong Wang, Ethalinda K.S. Cannon, Christopher Dwan, Anne-Francoise Lamblin, Jayprakash Vasdewani, Joann Mudge, Andrew Cook, John Gish, Foo Cheung, Steve Kenton, Timothy M. Kunau, Douglas Brown, Gregory D. May, Dongjin Kim, Douglas R. Cook, Bruce A. Roe, Chris D. Town, Nevin D. Young, and Ernest F. Retzel.
Plant Physiology, May 2005; 138(1):38-46.
"... for CCGB bioinformatics since targets are created for different platforms (Linux clusters, single machine use, TimeLogic DeCypher server) and these different targets must remain coherent and consistent. ..."
"Bioinformatics analysis and threading: A DeCypher hardware-accelerated bioinformatics system (TimeLogic, Inc.) was used to perform the Smith-Waterman, FrameSearch, and HMMER searches..."
PNAS March 29, 2005, 102(13):4795-4800 and Supporting Materials and Methods.
"Matches were detected with either the BLASTZ computer program or a hardware-optimized Smith-Waterman algorithm (TimeLogic, Carlsbad, CA)....Smith-Waterman alignments were generated by using a DeCypher machine (TimeLogic, Carlsbad, CA)."
GPR56 is a GPCR that is overexpressed in gliomas and functions in tumor cell adhesion.
Oncogene (2005) 24, 1673–1682. doi:10.1038/sj.onc.1208395 Published online 31 January 2005.
"Gene identification of clones was performed by an analysis of the sequences using BLAST and Smith–Waterman algorithms with NCBI, Unigene, Swiss-Prot/TrEMBL and Derwent databases with accelerated hardware (TimeLogic)."
Marian Seto, Marc Whitlow, Margaret A. McCarrick, Subha Srinivasan, Ying Zhu, Rene Pagila, Robert Mintzer, David Light, Anthony Johns, and Janet A. Meurer-Ogden.
Protein Sci., Dec 2004; 13(12):3172-3186.
"The human ASM protein sequence, corresponding to the predicted phosphoesterase domain (amino acid residues 201–472), was used to search for homologs. Three common search algorithms, BLAST, Smith-Waterman, and FASTA (Smith and Waterman 1981; Altschul et al. 1990; Pearson 1990), were used to search for possible templates in three protein databases—GenPept (database dated October 2000) (Benson et al. 2000), SwissProt (August 1999 version) (Bairoch and Boeckmann 1994), and Protein Data Bank (PDB; August 1999 version) (Berman et al. 2000)...With the exception of FASTA, all database searches were run using TimeLogic DeCypher."
"Abstract: We have developed a software package called Osprey for the calculation of optimal oligonucleotides for DNA sequencing and the creation of microarrays based on either PCR-products or directly spotted oligomers. It incorporates a novel use of position-specific scoring matrices, for the sensitive and specific identification of secondary binding sites anywhere in the target sequence. Using accelerated hardware is faster and more efficient than the traditional pairwise alignments used in most oligo-design software. Osprey consists of a module for target site selection based on user input, novel utilities for dealing with problematic sequences such as repeats, and a common code base for the identification of optimal oligonucleotides from the target list. Overall, these improvements provide a program that, without major increases in run time, reflects current DNA thermodynamics models, improves specificity and reduces the user's data preprocessing and parameterization requirements. Using a TimeLogic™ hardware accelerator, we report up to 50-fold reduction in search time versus a linear search strategy. Target sites may be derived from computer analysis of DNA sequence assemblies in the case of sequencing efforts, or genome or EST analysis in the case of microarray development in both prokaryotes and eukaryotes."
Plant Physiology, Jul 2004; 135(3):1179-1197.
"In the final BLAST iteration, the remaining legume-specific TCs were then compared to EST_others using the DeCypher Bioinformatics Accelerator running the Tera-BLAST hardware accelerated version of BLAST (TimeLogic, Crystal Bay, NV), which was housed in the Center for Computational Genomics and Bioinformatics at the University of Minnesota."
"...iRNA target gene prediction was performed by aligning miRNA sequences with target mRNA sequences using the TimeLogic implementation of the Smith-Waterman nucleotide-alignment algorithm..."
J. Virol., Jul 2004; 78(13):7023-7035.
"If difficulties were encountered identifying homologues with standard protein-protein BLAST (blastp) searches, further analysis was done using [...] Smith Waterman similarity searches using DeCypher with default settings."
J. Invest. Dermatol., Jul 2004; 123:23-33.
"The ClustalW sequence comparison program, decypher.stanford.edu, was used to align the protein sequences."
J. Biol. Chem., Feb 13, 2004; 279:5565-5572.
"...a comprehensive homology analysis was conducted using a Blast algorithm against the RefSeq (NCBI) data base on accelerated hardware (TimeLogic)."
Martin Madera, Christine Vogel, Sarah K. Kummerfeld, Cyrus Chothia, and Julian Gough.
Nucleic Acids Res., Jan 2004; 32(suppl 1):D235-D239.
"Genome assignments: Using TimeLogic DeCypher hardware, the library has been used to carry out assignments to predicted proteins from all completely sequenced genomes, the Swiss-Prot and TrEMBL databases and other sequence collections."
PNAS, Dec 23, 2003; 100(26):15670-15675.
"...The predicted proteins were submitted to Hidden Markov Model searches, implemented in timelogic (TimeLogic, Carlsbad, CA), to determine their multidomain PKS protein structures... ... The predicted proteins were submitted to Hidden Markov Model searches, implemented in TimeLogic (TimeLogic, Carlsbad, CA), to determine their multidomain structures..."
Current Protocols in Bioinformatics. 3.2.1-3.2.23. New York: John Wiley & Sons, Inc.
"Illustration of how insertion and deletion errors affect alignments generated by the six-frame-translated Smith-Waterman algorithm. Note that this example was generated on a DeCypher genomics accelerator, manufactured by TimeLogic."
"...on a TimeLogic DeCypher system one can specify a cutoff quality score or statistical probability score as well as the maximum numbers of scores and alignments to present"
"...the Timelogic implementation of Framesearch found on their DeCypher systems has a much more flexible provision for specifying which strand to search"
Eukaryot. Cell, Dec 2003; 2(6):1151-1161.
"... Conserved Pfam domains were identified by using the DeCypher hidden Markov model (protein sequence versus hidden Markov model) search algorithm ..."
"...Meloidogyne sequences from NCBI were analyzed using the Tera-BLAST Hardware Accelerated BLAST algorithm (TimeLogic...). Single FASTA files were submitted for three six-phase translated Tera-TBLASTX queries against six-phase translated C. elegans and Drosophila genomic databases..."
"The PFAM 7.0 database release, containing 3360 HMMs, was used to analyze gene sets for their protein domain content. For this analysis, the HMMER software package (Eddy, 1998) or its compatible implementations from Paracel and TimeLogic (http://www.timelogic.com) were run on a Linux computing cluster (150 CPUs, Linux Networks), a Paracel GENEMATCHER machine, and a TimeLogic Decypher machine, respectively."
NAR, September 1, 2003, 31(17):e106.
"...The TimeLogic system is currently implemented with MGView to accelerate the alignment operation ( www.timelogic.com ).... ... Together with the backbone genome nucleotide file, the TimeLogic BLAST report is used to produce two major PDF output files, MGMap and MGTrack ..."
"Gene identification of clones was performed by a rapid and comprehensive homology analysis of the sequenced ESTs using Blast and Smith–Waterman algorithms with NCBI, Unigene, Swiss-Prot/TrEMBL (GeneBio, Geneva, SW, USA), and Derwent patent (Alexandria, VA, USA) databases, and accelerated hardware (TimeLogic)."
Federico Simone, Roger T. Luo, Paul E. Polak, Joseph J. Kaberlein, and Michael J. Thirman.
Blood, Mar 15, 2003; 101(6):2355-2362.
"...were conducted with the basic local alignment search tool (BLAST) search algorithm and with the DeCypher II Similarity Search System. ... ... acid similarity previously observed between EAF1 and AF4 family members, we used the BLASTP and DeCypher II Smith Waterman algorithms to identify a comparable region of EAF2 with limited similarity to ..."
"Use of HMM to discover ePK domains: Local and global HMM models were built with the HMMer package (http://hmmer.wustl.edu) and were searched against sequence databases using the Decypher hardware-accelerated HMMer implementation from TimeLogic."
Bioinformatics, Sep 2002; 18: 1243 - 1249.
"... sanger.ac.uk/Software/Pfam/; Bateman et al. , 2002) using the HMMER2 software (http://hmmer.wustl.edu/) on a hardware accelerated Decypher box to build up a mapping of HOMSTRAD and Pfam families...."
"... position-specific score matrix (HMM) was then used to search the Arabidopsis protein database at the DeCypher Web site ( http://decypher2.stanford.edu/algo-hmm/ HMM_ha.html-ssi). ... ... that was generated by HMMbuild was used to search the Arabidopsis protein database from the DeCypher Web site [at Stanford] by pasting the model into the appropriate box..."
RNA, Jul 2002; 8: 913 - 923.
"... NM_001014) and S. cerevisiae S10 (Accession : NP_014936) are aligned with the ClustalW program (http://decypher.stanford.edu) and schematically presented with the Boxshade program + Identical residues are boxed in black ..."
Science, April 5, 2002, 296(5565):92-100.
"Timelogic's Decypher FrameSearch algorithm was used to detect and guide the correction of frameshifts caused by indels."
"...pattern matching; (4) HMMPfam from the HMMER package (http: //hmmer.wustl.edu/) or HMMS implemented on a Decypher machine from TimeLogic that scans sequences against the Pfam collection of protein domain HMMs (hidden ..."
"...the matrices of between-sequence distances are derived by the multiple alignments algorithm ClustalW, developed by Thompson et al. using the DeCypher server of TimeLogic Corporation."
J. Bacteriol., Jan 2002; 184:572-576.
"... The dendrogram was obtained by using CLUSTAL W and Decypher of Stanford University computer system..."
Evgeni M. Zdobnov and Rolf Apweiler.
"[Pfam and SMART domains identified using TimeLogic™ HMM Search.]"
"Multiple sequence alignments were obtained by CLUSTALW running at the Decypher hardware accelerator (www.timelogic.com)."
PNAS July 31, 2001; 98(16):8966-8971.
"Amino acid sequences for each receptor spanning from the start of TMI to the end of TMVII were aligned by using the CLUSTALW algorithm and the tree constructed by the NJ method on a DecypherII Bioaccelerator (TimeLogic, Reno, NV)."
Blood July 1, 2001, 98(1):201-209.
"Database searches were conducted with the BLAST search algorithm and with the DeCypher II Similarity Search System."
Infection and Immunity, May 2001, 69(5):3271-3285.
"Each ORF was initially searched against the GenPept protein database using the DeCypher II system, to determine identity or match with known proteins. After subsequent inspection and further analysis of many of the ORFs, annotations were created."
J Virol. 2000 December; 74(23): 11377–11387.
"Sequences were compared by CLUSTALW multiple-sequence alignment using the DeCypher bioinformatics supercomputer (Center for Molecular and Genetic Medicine, Stanford University)."
Nucl. Acids Res. (2000) 28(1):31-32.
"Frame Search can be used to search a protein query sequence against a dynamically translated nucleotide database. As a consequence of the Smith–Waterman basis of this algorithm and the dynamic translation of the query sequence or target database, Frame Search is a computationally intensive algorithm. However, based upon internal testing and benchmarking of Frame Search on the Decypher system, we have found that it is comparable in speed to tblastx searches."
"Genes were considered homologs if the blast score was less than e?15 and aligned over >30% of the vertebrate protein sequence. In some cases, two genomic sequences for a single gene were identified due to a gap in the genomic sequence, in which case the blast scores for both genomic sequences are listed. When known Drosophila genes were previously identified, the Drosophila name is in bold, and the percent identity/similarity was determined using the Smith-Waterman algorithm (http://www.timelogic.com/)."
"Searches of the protein databases for amino acid similarities were performed using the DeCypher II system (TimeLogic Inc.) to assign known functions or suggest functions for new ORFs."
Nucleic Acids Res. (2000); 28(1):87-90.
"...and it will soon be possible to apply to these sequences the more advanced similarity search algorithms available on NCGR’s TimeLogic server..."
Nucl. Acids Res. (1999) 27(1):35-38.
"A TimeLogic DeCypher II was recently acquired to provide a server for homology searching using several algorithms... The DeCypher includes accelerated versions of Smith-Waterman, Frame Search, Symmetric Frame Independent and Profile Search that will become publicly available for searching data from GSDB during the first half of 1999."
Journal of Virology, May 1999, 73(5):4197-4207 and Table.
"Alignment of gK proteins from alphaherpesviruses with the DeCypher II Smith-Waterman Example program (Center for Molecular and Genetic Medicine, Stanford University) shows substantial similarity to VZV. aa, amino acid(s)."
Stephen A. Chervitz, Erich T. Hester, Catherine A. Ball, Kara Dolinski, Selina S. Dwight, Midori A. Harris, Gail Juvik, Alice Malekian, Shannon Roberts, TaiYun Roe, Charles Scafe, Mark Schroeder, Gavin Sherlock, Shuai Weng, Yan Zhu, J. Michael Cherry and David Botstein.
Nucleic Acids Research (1999) 27(1)74-78.
"Smith-Waterman comparisons were conducted on a TimeLogic DeCypher II machine using the affine Smith-Waterman application."
Luther E. Lindler, Gregory V. Plano, Valerie Burland, George F. Mayhew, and Frederick R. Blattner.
Infection and Immunity, December 1998, 66(12):5731-5742.
"For the first pass, amino acid sequences were searched against the current GenPept database by using the BLOSUM62 matrix by the DeCypher II System (TimeLogic, Inc., Incline Village, Nev.)."
DNA Sequencing and Analysis of the Low-Ca2+-Response Plasmid pCD1 of Yersinia pestis KIM5.
Infection and Immunity, October 1998, 66(10):4611-4623.
"ORF amino acid sequences were searched against SWISS-PROT 34 by using the BLOSUM26 matrix, with the DeCypher II System (TimeLogic Inc.)."
Mechanisms of Development, September 1998, 77(2):95-141.
"Sequences were assembled and analyzed for redundant clones using the DeCypher II PC board and accompanying software (Time Logic)."
Nucl. Acids Res. (1998) 26(18):4196-4204.
"ORF amino acid sequences were searched against SWISS-PROT 34 and GenPept 104 using the BLOSUM62 matrix and the Smith-Waterman algorithm accelerated by the DeCypher II system (TimeLogic Inc.) to assign known functions or suggest functions for new ORFs."
Infect Immun, August 1998, 66(8):3810-3817.
"Each ORF was annotated based on protein sequence searches (DeCypherII hardware/software system; TimeLogic, Inc.) against a combined SwissProt release 34 and trEMBLSP release 1 database."
Science 5 September 1997: 277(5331):1453-1462.
"The function of new translated sequences was imputed from sequence similarity... Similarity searches were conducted using both the DeCypher II hardware-software system (Time Logic Inc., Incline Village, NV) and the PepPepSearch program of the Darwin suite at Zurich..."

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