bluuebunny/crossref_metadata_2025_split huggingface dataset:
Flexibility of the genetic code with respect to DNA structure
Authors: Baisnée Pierre-François , Baldi Pierre , Brunak Søren , Pedersen Anders Gorm 
Published: July 2002

Abstract
Motivation: The primary function of DNA is to carry genetic information through the genetic code. DNA, however, contains a variety of other signals related, for instance, to reading frame, codon bias, pairwise codon bias, splice sites and transcription regulation, nucleosome positioning and DNA structure. Here we study the relationship between the genetic code and DNA structure and address two questions. First, to which degree does the degeneracy of the genetic code and the acceptable amino acid substitution patterns allow for the superimposition of DNA structural signals to protein coding sequences? Second, is the origin or evolution of the genetic code likely to have been constrained by DNA structure?
Results: We develop an index for code flexibility with respect to DNA structure. Using five different di- or tri-nucleotide models of sequence-dependent DNA structure, we show that the standard genetic code provides a fair level of flexibility at the level of broad amino acid categories. Thus the code generally allows for the superimposition of any structural signal on any protein-coding sequence, through amino acid substitution. The flexibility observed at the level of single amino acids allows only for the superimposition of punctual and loosely positioned signals to conserved amino acid sequences. The degree of flexibility of the genetic code is low or average with respect to several classes of alternative codes. This result is consistent with the view that DNA structure is not likely to have played a significant role in the origin and evolution of the genetic code.
Contact: pfbaldi@ics.uci.edu; baisnee@ics.uci.edu; brunak@cbs.dtu.dk; gorm@cbs.dtu.dk
* To whom correspondence should be addressed.
MetaFam: a unified classification of protein families. II.

Schema and query capabilities
Authors: Shoop Elizabeth , Silverstein Kevin A. T. , Johnson James E. , Retzel Ernest F. 
Published: July 2002

Abstract
Motivation: Protein sequence and family data is accumulating at such a rapid rate that state-of-the-art databases and interface tools are required to aid curators with their classifications. We have designed such a system, MetaFam, to facilitate the comparison and integration of public protein sequence and family data. This paper presents the global schema, integration issues, and query capabilities of MetaFam.
Results: MetaFam is an integrated data warehouse of information about protein families and their sequences. This data has been collected into a consistent global schema, and stored in an Oracle relational database. The warehouse implementation allows for quick removal of outdated data sets. In addition to the relational implementation of the primary schema, we have developed several derived tables that enable efficient access from data visualization and exploration tools. Through a series of straightforward SQL queries, we demonstrate the usefulness of this data warehouse for comparing protein family classifications and for functional assignment of new sequences.
Availability: Access to the MetaFam database is provided through a Java applet called MetaFamView, which can be run from the MetaFam web site at http://www.metafam.ahc.umn.edu/. Access to the relational data via named Oracle accounts can be arranged with the authors. Arrangements can also be made to obtain the data in Oracle ‘export dump’ format.
Contact: metafam@ahc.umn.edu
Supplementary information: The complete relational schema, integration scripts, and analysis queries are available from the authors.
* To whom correspondence should be addressed.
Genview and Gencode : a pair of programs to

test theories of genetic code evolution
Authors: Ronneberg T. Andrew , Freeland Stephen J. , Landweber Laura F. 
Published: July 2002

Abstract
Summary: Genview and Gencode are tools for testing the adaptive nature of a genetic code under different assumptions about patterns of genetic error and the nature of amino acid similarity. Genview provides a user friendly, point-and-click interface by which a user may reproduce and extend analysis of the adaptive properties of the standard genetic code or any of its secondary derivatives. Genview is a graphical user interface (GUI) program which runs on Linux, Unix®and Microsoft Windows®platforms and is based on the GTK\batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(+\) \end{document}toolkit. Genview outputs ASCII configuration files which are interpreted by Gencode to perform an analysis. Gencode is available for the same platforms as Genview.
Availability: Online documentation can be found at http://rnaworld.princeton.edu/genview/documentation. The source code can be downloaded from http://rnaworld.princeton.edu/genview/
Contact: sfreelan@princeton.edu
* To whom correspondence should be addressed.
Limits of homology detection by pairwise sequence comparison
Authors: Spang Rainer , Vingron Martin 
Published: July 2002

Abstract
Motivation: Noise in database searches resulting from random sequence similarities increases as the databases expand rapidly. The noise problems are not a technical shortcoming of the database search programs, but a logical consequence of the idea of homology searches. The effect can be observed in simulation experiments.
Results: We have investigated noise levels in pairwise alignment based database searches. The noise levels of 38 releases of the SwissProt database, display perfect logarithmic growth with the total length of the databases. Clustering of real biological sequences reduces noise levels, but the effect is marginal.
Contact: rainer@stat.duke.edu; m.vingron@dkfz-heidelberg.de
2 To whom correspondence should be addressed. Pressent address: Duke University, Institute of Statistics and Decision Sciences, Box 90251 Duke University, Durham, NC 27708-0251, USA.
BioMolQuest: integrated database-based retrieval of protein

structural and functional information
Authors: Bukhman Yury V. , Skolnick Jeffrey 
Published: July 2002

Abstract
Motivation: Information about a particular protein or protein family is usually distributed among multiple databases and often in more than one entry in each database. Retrieval and organization of this information can be a laborious task. This task is complicated even further by the existence of alternative terms for the same concept.
Results: The PDB, SWISS-PROT, ENZYME, and CATH databases have been imported into a combined relational database, BioMolQuest. A powerful search engine has been built using this database as a back end. The search engine achieves significant improvements in query performance by automatically utilizing cross-references between the legacy databases. The results of the queries are presented in an organized, hierarchical way.
Availability: http://bioinformatics.danforthcenter.org/yury/public/home.html. Unavailable for commercial users.
Contact: skolnick@danforthcenter.org
* To whom correspondence should be addressed.
Database verification studies of SWISS-PROT and GenBank
Authors: Karp Peter D. , Paley Suzanne , Zhu Jingchun 
Published: July 2002

Abstract
Problem statement: We have studied the relationships among SWISS-PROT, TrEMBL, and GenBank with two goals. First is to determine whether users can reliably identify those proteins in SWISS-PROT whose functions were determined experimentally, as opposed to proteins whose functions were predicted computationally. If this information was present in reasonable quantities, it would allow researchers to decrease the propagation of incorrect function predictions during sequence annotation, and to assemble training sets for developing the next generation of sequence-analysis algorithms. Second is to assess the consistency between translated GenBank sequences and sequences in SWISS-PROT and TrEMBL.
Results: (1) Contrary to claims by the SWISS-PROT authors, we conclude that SWISS-PROT does not identify a significant number of experimentally characterized proteins. (2) SWISS-PROT is more incomplete than we expected in that version 38.0 from July 1999 lacks many proteins from the full genomes of important organisms that were sequenced years earlier. (3) Even if we combine SWISS-PROT and TrEMBL, some sequences from the full genomes are missing from the combined dataset. (4) In many cases, translated GenBank genes do not exactly match the corresponding SWISS-PROT sequences, for reasons that include missing or removed methionines, differing translation start positions, individual amino-acid differences, and inclusion of sequence data from multiple sequencing projects. For example, results show that for Escherichia coli , 80.6% of the proteins in the GenBank entry for the complete genome have identical sequence matches with SWISS-PROT/TrEMBL sequences, 13.4% have exact substring matches, and matches for 4.1% can be found using BLAST search; the remaining 2.0% of E.coli protein sequences (most of which are ORFs) have no clear matches to SWISS-PROT/TrEMBL. Although many of these differences can be explained by the complexity of the DB, and by the curation processes used to create it, the scale of the differences is notable.
Contact: pkarp@ai.sri.com
* To whom correspondence should be addressed.
SCORE: predicting the core of protein models
Authors: Deane Charlotte M. , Kaas Quentin , Blundell Tom L. 
Published: July 2002

Abstract
Motivation: The prediction of the regions of homology models that can be ‘restrained by’ or ‘copied from’ the basis structures is a vital step in correct model generation, because these regions are the models most accurate part. However, there is no ideal method for the identification of their limits. In most algorithms their length depends on the number of family members and definitions of secondary structure.
Results: The algorithm SCORE steps away from the conventional definitions of the core to identify from large numbers of basis structures those regions that can be considered structurally related to a target sequence. The use of \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \({\phi},\ {\psi}\) \end{document}constraints to accurately pinpoint the regions that are conserved across a family and environmentally constrained substitution tables to extend these regions allows SCORE to rapidly (generally in under 1 s, an order of magnitude faster than methods such as MODELLER) identify and build the core of homology models from the alignments of the target sequence to the basis structures. The SCORE algorithm was used to build 114 model cores. In only two cases was the core size less than 50% of the structure and all the cores built had an RMSD of 3.7 Âor less to the target structure.
Availability: The algorithm is available upon request.
Contact: charlotte@cryst.bioc.cam.ac.uk
* To whom correspondence should be addressed.
The HIB database of annotated UniGene clusters
Authors: Geier Birgitta , Kastenmüller Gabi , Fellenberg Matthias , Mewes Hans-Werner , Morgenstern Burkhard 
Published: July 2002

Abstract
Summary: The HumanInfoBase (HIB) is a database of putative human gene transcripts. UniGene clusters are assembled, and the resulting consensus sequences are submitted to the PEDANT software system (Frishman,D., Albermann,K., Hani,J., Heumann,K., Metanomski,A., Zollner,A. and Mewes,H.-W., 2001, Bioinformatics , 17, 44–57) for fully automatic sequence analysis and annotation. Predicted transcripts are classified using a variety of functional and structural categories, and hyperlinks to various databases are provided for additional information. A WWW-based graphical user interface represents the assembly process as well as functionally important sites in the putative transcripts.
Availability: http://mips.gsf.de/proj/human/
Contact: morgenst@mips.gsf.de
* To whom correspondence should be addressed.
SeWeR: a customizable and integrated dynamic HTML interface to

bioinformatics services
Authors: Kumar Basu Malay 
Published: July 2002

Abstract
Summary: Se quence analysis using We b R esources (SeWeR) is an integrated, Dynamic HTML (DHTML) interface to commonly used bioinformatics services available on the World Wide Web. It is highly customizable, extendable, platform neutral, completely server-independent and can be hosted as a web page as well as being used as stand-alone software running within a web browser.
Availability: The web version of SeWeR can be freely accessed from http://www.bioinformatics.org/sewer/ or http://iubio.bio.indiana.edu/webapps/SeWeR/, and also from several mirror sites all over the world (a full listing is available on the SeWeR web page).It can also be downloaded under GNU General Public License from ftp://iubio.bio.indiana.edu/molbio/analyze/sewer.zip.
Contact: curiouser@ccmb.ap.nic.in
Identifying the 3′-terminal exon in

human DNA
Authors: Tabaska Jack E. , Davuluri Ramana V. , Zhang Michael Q. 
Published: July 2002

Abstract
Motivation: We present JTEF, a new program for finding 3′ terminal exons in human DNA sequences. This program is based on quadratic discriminant analysis, a standard non-linear statistical pattern recognition method. The quadratic discriminant functions used for building the algorithm were trained on a set of 3′ terminal exons of type 3tuexon (those containing the true STOP codon).
Results: We showed that the average predictive accuracy of JTEF is higher than the presently available best programs (GenScan and Genemark.hmm) based on a test set of 65 human DNA sequences with 121 genes. In particular JTEF performs well on larger genomic contigs containing multiple genes and significant amounts of intergenic DNA. It will become a valuable tool for genome annotation and gene functional studies.
Availability: JTEF is available free for academic users on request from ftp://cshl.org/pub/science/mzhanglab/JTEF and will be made available through the World Wide Web (http://argon.cshl.org/).
Contact: mzhang@cshl.org; ramana@cshl.org
* To whom correspondence should be addressed.
2 Present address: Monsanto Company, 800 North Lindbergh, St Louis, MO 63167, USA.
Genotype transposer: automated genotype manipulation for
linkage disequilibrium analysis
Authors: Cox David G. , Canzian Federico 
Published: July 2002

Abstract
Summary: The purpose of this work is to provide the modern molecular geneticist with tools to perform more efficient and more accurate analysis of the genotype data they produce. By using Microsoft Excel macros written in Visual Basic, we can translate genotype data into a form readable by the versatile software ‘Arlequin’, read the Arlequin output, calculate statistics of linkage disequilibrium, and put the results in a format for viewing with the software ‘GOLD’.
Availability: The software is available by FTP at: ftp://xcsg.iarc.fr/cox/Genotype_Transposer/.
Contact: cox@iarc.fr
Supplementary information: Detailed instruction and examples are available at: ftp://xcsg.iarc.fr/cox/Genotype&_Transposer/. Arlequin is available at: http://lgb.unige.ch/arlequin/. GOLD is available at: http://www.well.ox.ac.uk/asthma/GOLD/.
* To whom correspondence should be addressed.
DBAli: a database of protein structure alignments
Authors: Martı́-Renom Marc
A. , Ilyin Valentin A. , Sali Andrej 
Published: July 2002

Abstract
Summary: The DBAli database includes approximately 35000 alignments of pairs of protein structures from SCOP (Lo Conte et al. , Nucleic Acids Res. , 28, 257–259, 2000) and CE (Shindyalov and Bourne, Protein Eng. , 11, 739–747, 1998). DBAli is linked to several resources, including Compare3D (Shindyalov and Bourne, http://www.sdsc.edu/pb/software.htm, 1999) and ModView (Ilyin and Sali, http://guitar.rockefeller.edu/ModView/, 2001) for visualizing sequence alignments and structure superpositions. A flexible search of DBAli by protein sequence and structure properties allows construction of subsets of alignments suitable for a number of applications, such as benchmarking of sequence–sequence and sequence–structure alignment methods under a variety of conditions.
Availability: http://guitar.rockefeller.edu/DBAli/
Contact: sali@rockefeller.edu; http://guitar.rockefeller.edu
* To whom correspondence should be addressed.
PathFinder: reconstruction and dynamic visualization of
metabolic pathways
Authors: Goesmann Alexander , Haubrock Martin , Meyer Folker , Kalinowski Jörn , Giegerich Robert 
Published: July 2002

Abstract
Motivation: Beyond methods for a gene-wise annotation and analysis of sequenced genomes new automated methods for functional analysis on a higher level are needed. The identification of realized metabolic pathways provides valuable information on gene expression and regulation. Detection of incomplete pathways helps to improve a constantly evolving genome annotation or discover alternative biochemical pathways. To utilize automated genome analysis on the level of metabolic pathways new methods for the dynamic representation and visualization of pathways are needed.
Results: PathFinder is a tool for the dynamic visualization of metabolic pathways based on annotation data. Pathways are represented as directed acyclic graphs, graph layout algorithms accomplish the dynamic drawing and visualization of the metabolic maps. A more detailed analysis of the input data on the level of biochemical pathways helps to identify genes and detect improper parts of annotations. As an Relational Database Management System (RDBMS) based internet application PathFinder reads a list of EC-numbers or a given annotation in EMBL- or Genbank-format and dynamically generates pathway graphs.
Availability: The software PathFinder will be made available on the Bielefeld Bioinformatics WebServer under the following URL: http://bibiserv.TechFak.Uni-Bielefeld.DE/pathfinder/. The source code is available upon request and will eventually be released under GPL.
Contact: Alexander.Goesmann@Genetik.Uni-Bielefeld.DE
Using biplots to interpret gene expression patterns in plants
Authors: Chapman Scott , Schenk Peer , Kazan Kemal , Manners John 
Published: July 2002

Abstract
Summary: Plant biologists in fields of ecology, evolution, genetics and breeding frequently use multivariate methods. This paper illustrates Principal Component Analysis (PCA) and Gabriel’s biplot as applied to microarray expression data from plant pathology experiments.
Availability: An example program in the publicly distributed statistical language R is available from the web site (www.tpp.uq.edu.au) and by e-mail from the contact.
Contact: scott.chapman@csiro.au
CIT: identification of differentially expressed clusters of
genes from microarray data
Authors: Rhodes Daniel R. , Miller Jeremy C. , Haab Brian B. , Furge Kyle A. 
Published: July 2002

Abstract
Summary: Cluster Identification Tool (CIT) is a microarray analysis program that identifies differentially expressed genes. Following division of experimental samples based on a parameter of interest, CIT uses a statistical discrimination metric and permutation analysis to identify clusters of genes or individual genes that best differentiate between the experimental groups. CIT integrates with the freely available CLUSTER and TREEVIEW programs to form a more complete microarray analysis package.
Availability: A Windows® binary executable is freely available at http://www.vai.org/vari/bioinformatics.htm
Contact: Kyle.Furge@vai.org
Supplementary information: http://www.vai.org/vari/bioinfomatics.htm
* To whom correspondence should be addressed.
ISEApeaks: an Excel platform for GeneScan and Immunoscope data
retrieval, management and analysis
Authors: Collette A. , Six A. 
Published: July 2002

Abstract
Summary: ISEApeaks retrieves and handles DNA sequencer raw data (peak area and nucleotidic length). This Macintosh package efficiently interfaces GeneScan and Immunoscope softwares to Excel by extracting data from scattered files, organizing data and gathering it into a unique peak database for all samples.
Availability: ISEApeaks is available upon request from the authors.
Contact: collette@pasteur.fr; askc@pasteur.fr, http://www.pasteur.fr/recherche/unites/Imchan/iseapeakuk.html
* To whom correspondence should be addressed.
Interactive InterPro-based comparisons of proteins in whole
genomes
Authors: Kanapin A. , Apweiler R. , Biswas M. , Fleischmann W. , Karavidopoulou Y. , Kersey P. , Kriventseva E. V. , Mittard V. , Mulder N. , Oinn T. , Phan I. , Servant F. , Zdobnov E. 
Published: July 2002

Abstract
Motivation: The SWISS-PROT group at the EBI has developed the Proteome Analysis Database utilizing existing resources and providing comprehensive and integrated comparative analysis of the predicted protein coding sequencesof the complete genomes of bacteria, archaea and eukaryotes. The Proteome Analysis Database is accompanied by a program that has been designed to carry out interactive InterPro proteome comparisons for any one proteome against any other one or more of the proteomes in the database.
Availability: http://www.ebi.ac.uk/proteome/comparisons.html
Contact: alex@ebi.ac.uk; proteome@ebi.ac.uk
* To whom all correspondence should be addressed.
GeneANOVA—gene expression analysis of variance
Authors: Didier G. , Brézellec P. , Remy E. , Hénaut A. 
Published: July 2002

Abstract
Summary: GeneANOVA is an ANOVA-based software devoted to the analysis of gene expression data.
Availability: GeneANOVA is freely available on request for non-commercial use.
Contact: didier@genopole.cnrs.fr
Gene structure identification with MyGV using cDNA
evidence and protein homologs to improve ab initio
predictions
Authors: Zhu Wei , Brendel Volker 
Published: July 2002

Abstract
Summary: MyGV is an application to visualize (potentially genome-scale) gene structure annotation and prediction. The output of any external gene prediction program can be easily converted to a generalized format for input into MyGV. The application displays all input simultaneously in graphical representation, with a toggle option for a text-based view. Zooming capabilities allow detailed comparisons for specific genome locations. The tool is particularly helpful for refinement of ab initio predicted gene structures by spliced alignment with cDNA or protein homologs.
Availability: The program was written in Java and is freely available to non-commercial users by electronic download from http://bioinformatics.iastate.edu/bioinformatics2go/MyGV.
Contact: vbrendel@iastate.edu
GP3: GenePix post-processing program for automated analysis of raw microarray data
Authors: Fielden M. R. , Halgren R. G. , Dere E. , Zacharewski T. R. 
Published: July 2002

Abstract
Summary: Here we describe an automated and customizable program to correct, filter and normalize raw microarray data captured using GenePix, a commonly used microarray image analysis application. Files can be processed individually or in batch mode for increased throughput. User defined inputs specify the stringency of data filtering and the method and conditions of normalization. The output includes gene summaries for replicate spots and descriptive statistics for each experiment. The source code (Perl) can also be adapted to handle raw data output from other image analysis applications.
Availability: http://bch.msu.edu/~zacharet/microarray/GP3.html
Contact: tzachare@msu.edu
Supplementary information: http://bch.msu.edu/~zacharet/microarray/GP3.html
* To whom correspondence should be addressed.