recursal/Fanatic-Fandom huggingface dataset:
Germline mutation

A **germline mutation** refers to the "presence of an altered gene within the egg or sperm (germ cell), such that the altered gene can be passed to subsequent generations".

## See Also

* De novo mutation
* Germline
* Germline mosaicism

## References

1. ↑ Pagon RA, Adam MP, Ardinger HH, et al., editors. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2015. *Illustrated Glossary*. Available from: http://www.ncbi.nlm.nih.gov/books/NBK5191/
Glycomics

**Glycomics** is the study of the glycome.

## References

1. ↑ Bertozzi CR, Sasisekharan R. Glycomics. In: Varki A, Cummings RD, Esko JD, et al., editors. *Essentials of Glycobiology*. 2nd edition. Cold Spring Harbor (NY): Cold Spring Harbor Laboratory Press; 2009. Chapter 48. Available from: http://www.ncbi.nlm.nih.gov/books/NBK1965/
Gel filtration chromatography

**Gel filtration chromatography** (also referred to as **molecular exclusion chromatography** or **gel permeation chromatography**) is a process which "sep[]arates proteins, peptides, and oligonucleotides on the basis of size. Molecules move through a bed of porous beads, diffusing into the beads to greater or lesser degrees. Smaller molecules diffuse further into the pores of the beads and therefore move through the bed more slowly, while larger molecules enter less or not at all and thus move through the bed more quickly. Both molecular weight and three-dimensional shape contribute to the degree of retention".

## References

1. ↑ "Gel Filtration Chromatography." *Sigma-Aldrich*. Sigma-Aldrich Co. LLC, n.d. Web. 11 Oct. 2015.
Drug-drug interaction

A **drug-drug interaction** is an event which occurs "when a drug interacts, or interferes, with another drug".

## References

1. ↑ "Frequently Asked Questions (FAQs) About Drug-Drug Interactions Involving OTC Medications." BeMedWise. National Council on Patient Information and Education, 05 Feb. 2013. Web. 03 Sept. 2015.
Cytoplasm

**Cytoplasm** is a "thick solution that fills each cell and is enclosed by the cell membrane. It is mainly composed of water, salts, and proteins. In eukaryotic cells, the cytoplasm includes all of the material inside the cell and outside of the nucleus. All of the organelles in eukaryotic cells, such as the nucleus, endoplasmic reticulum, and mitochondria, are located in the cytoplasm. The portion of the cytoplasm that is not contained in the organelles is called the cytosol. Although cytoplasm may appear to have no form or structure, it is actually highly organized. A framework of protein scaffolds called the cytoskeleton provides the cytoplasm and the cell with their structure."

## References

1. ↑ "Cytoplasm." *Scitable*. Nature Education, 2014. Web. 9 Aug. 2016.
GenPept

**GenPept** is an "archival database of protein sequences translated from ORFs annotated in GenBank; the basis for the NR database".

## External Links

* Bio::DB::GenPept - search.cpan.org
* GenPept documentation

## References

1. ↑ Koonin EV, Galperin MY. *Sequence - Evolution - Function: Computational Approaches in Comparative Genomics*. Boston: Kluwer Academic; 2003. Glossary. Available from: http://www.ncbi.nlm.nih.gov/books/NBK20257/
DNA

**DNA** (**deoxyribonucleic acid**) is a "substance contained in all cells that serves as a template for all cellular activity. Its sugar molecule is deoxyribose (hence its name), and it consists of the four nucleobases adenine, cytosine, guanine, and thymine, whose order determine its primary structure".

## References

1. ↑ "DNA - Glossary." *ROSALIND*. N.p., n.d. Web. 07 June 2015.
Computer programming

**Computer programming** (usually referred to simply as **programming** and sometimes written as **computer-programming**) is "the process of designing and writing a computer program in a programming language, such as a machine language, an assembler language, or a higher level programming language (e.g., Ada, BASIC, C, C++)".

## External Links

* Computer Programming - Wikibooks
* Computer Programming|Khan Academy

## References

1. ↑ Moursund, D. G. "Chapter 9: Computer Programming." *Increasing Your Expertise as a Problem Solver: Some Roles of Computers*. University of Oregon, 2002. Web. 07 June 2015.
FASTA file

A **FASTA file** is a text file in which each sequence it contains begins with a single-line description, followed by lines of sequence data. The single-line description contains a greater-than (>) symbol in the first column, followed by the sequence name.

## References

1. ↑ "FASTA." *Integrative Genomics Viewer*. Broad Institute, 2013. Web. 14 Oct. 2015.
Electrostatic force

**Electrostatic force** or **interaction** (also known as **Coulomb force** or **Coulomb interaction**) is "attraction or repulsion of particles or objects because of their electric charge".

## External Links

* Coulomb Force -- from Eric Weisstein's World of Physics

## References

1. ↑ "Coulomb force". *Encyclopædia Britannica*. *Encyclopædia Britannica Online*. Encyclopædia Britannica Inc., 2015. Web. 02 Sep. 2015
<http://www.britannica.com/science/Coulomb-force>.
Circular dichroism

**Circular dichroism** (**CD**) is the "difference in the absorption of left-handed circularly polarised light (L-CPL) and right-handed circularly polarised light (R-CPL) and occurs when a molecule contains one or more chiral chromophores (light-absorbing groups)".

## References

1. ↑ "Circular Dichroism (CD) Spectroscopy." *Applied Photophysics*. Applied Photophysics Ltd, n.d. Web. 27 Sept. 2015.
Fluxomics

**Fluxomics** is the "discipline that analyzes the fluxome as one part of systems biology," but may also refer to an "approach [used] to identify the genes that affect the fluxes which control the steady state of a single metabolite (using FRET nanosensors)".

## Further Reading

* Winter, Gal, and Jens O. Krömer. "Fluxomics - Connecting ‘omics Analysis and Phenotypes." *Environmental Microbiology* 15.7 (2013): 1901-916. Print.

## References

1. ↑ Wiechert, Wolfgang et al. “Fluxomics: Mass Spectrometry versus Quantitative Imaging.” *Current opinion in plant biology* 10.3 (2007): 323–330. PMC. Web. 2 Sept. 2015.
Expressed sequence tag

## Further Reading

* Folta, Kevin M et al. “Expressed Sequence Tags (ESTs) and Simple Sequence Repeat (SSR) Markers from Octoploid Strawberry (*Fragaria* × *ananassa*).” *BMC Plant Biology* 5 (2005): 12. *PMC*. Web. 23 Oct. 2015.
* Nagaraj, S. H., R. B. Gasser, and S. Ranganathan. "A Hitchhiker's Guide to Expressed Sequence Tag (EST) Analysis." *Briefings in Bioinformatics* 8.1 (2006): 6-21. Print.
Coding region

The **coding region** (usually shortened from the **coding region of a gene**; sometimes erroneously referred to as the coding sequence, which is somewhat more general, or correctly as a **coding DNA sequence**, but abbreviated somewhat ambiguously as CDS) is a "sequence of DNA consisting of a series of nucleotide bases (code) giving rise to the mature messenger RNA that will be translated into the specific amino acids of the protein product".

## References

1. ↑ "Coding Region - Glossary Entry." *Genetics Home Reference*. National Institutes of Health (NIH), 19 Oct. 2015. Web. 22 Oct. 2015.
Complete binary tree

A **complete binary tree** is a "binary tree in which every level (depth), except possibly the deepest, is completely filled. At depth *n*, the height of the tree, all nodes must be as far left as possible".

## References

1. ↑ Paul E. Black, "complete binary tree", in *Dictionary of Algorithms and Data Structures* [online], Vreda Pieterse and Paul E. Black, eds. 27 August 2014. (accessed 21 Oct. 2015) Available from: http://www.nist.gov/dads/HTML/completeBinaryTree.html
Genetic predisposition

**Genetic predisposition** (also referred to as **genetic susceptibility**) refers to "increased susceptibility to a particular disease due to the presence of one or more gene mutations associated with an increased risk for the disease and/or a family history that indicates an increased risk for the disease".

## References

1. ↑ Pagon RA, Adam MP, Ardinger HH, et al., editors. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2015. *Illustrated Glossary*. Available from: http://www.ncbi.nlm.nih.gov/books/NBK5191/
ENCODE

The **ENCODE Project** (**Encyclopedia of DNA Elements**, sometimes also referred to as the **ENCODE Consortium**) is an "international collaboration of research groups funded by the National Human Genome Research Institute (NHGRI)". Its goal is to "build a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which a gene is active".

## External Links

* ENCODE at UCSC
* ENCODE Project

## References

1. ↑ 1.0 1.1 "ENCODE: Encyclopedia of DNA Elements." *ENCODE*. Stanford University, 2015. Web. 07 June 2015.
Dephosphorylation

**Dephosphorylation** refers to the "removal of a phosphate group from an organic compound".

## References

1. ↑ "dephosphorylation." *Random House Kernerman Webster’s College Dictionary*. 2010. 2010 K Dictionaries Ltd. Copyright 2005, 1997, 1991 by Random House, Inc. 2 Nov. 2015 <http://www.thefreedictionary.com/dephosphorylation>
Conformational isomer

A **conformational isomer** (also referred to as a **conformer**, **rotational isomer** or **rotamer**) is a stereoisomer produced by rotation (twisting) about σ bonds, and is often rapidly interconverting at room temperature.

## References

1. ↑ Hunt, Ian, and Rick Spinney. "Ch 3 : Conformational Isomers." *Organic Chemistry On-Line Learning Center*. Dr. Ian Hunt, Department of Chemistry, University of Calgary, n.d. Web. 04 Oct. 2015.
Complimentarity determining region

A **complimentarity determining region** (**CDR**) or **hypervariable loop** is a restricted region within the variable region of an antibody that bind to antigenic determinants.

## Further Reading

* Martin, A. C., J. C. Cheetham, and A. R. Rees. "Modeling Antibody Hypervariable Loops: A Combined Algorithm." *Proceedings of the National Academy of Sciences* 86.23 (1989): 9268-272. Print.

## References

1. ↑ "complementarity-determining region (CDR)." *Saunders Comprehensive Veterinary Dictionary, 3 ed.*. 2007. Elsevier, Inc. 12 Oct. 2015 <http://medical-dictionary.thefreedictionary.com/complementarity-determining+region+(CDR)>
External sort

**External sort** refers to "any sort algorithm that uses external memory, such as tape or disk, during the sort. Since most common sort algorithms assume high-speed random access to all intermediate memory, they are unsuitable if the values to be sorted don't fit in main memory".

## References

1. ↑ Paul E. Black, "external sort", in *Dictionary of Algorithms and Data Structures* [online], Vreda Pieterse and Paul E. Black, eds. 23 December 2013. (accessed 16 Oct. 2015) Available from: http://www.nist.gov/dads/HTML/externalsort.html
Chaperonin

A **chaperonin** is a "molecular complex composed of multiple heat shock protein subunits that assemble into double ring structures. Chaperonins function within the cytoplasm to refold damaged proteins".

## References

1. ↑ "chaperonin." *Farlex Partner Medical Dictionary*. 2012. Farlex 12 Oct. 2015 <http://medical-dictionary.thefreedictionary.com/chaperonin>
FASTA

**FASTA** (an abbreviation of **Fast-All**, "All" referring to "Protein" and "Nucleotide" in this context) is a "more sensitive derivative of the FASTP program, which can be used to search protein or DNA sequence data bases and can compare a protein sequence to a DNA sequence data base by translating the DNA data base as it is searched."

## External Links

* FASTA/SSEARCH/GGSEARCH/GLSEARCH < Sequence Similarity Searching < EMBL-EBI
* UVA FASTA Server

## References

1. ↑ Pearson, W R, and D J Lipman. “Improved Tools for Biological Sequence Comparison.” *Proceedings of the National Academy of Sciences of the United States of America* 85.8 (1988): 2444–2448. Print.
Computational evolutionary biology

**Computational evolutionary biology** is a "study that applies the discipline and techniques of computer science and mathematics to explore the processes of change in populations of organisms, especially taxonomy, paleontology, ethology, population genetics and ecology".

## External Links

* Computational Evolutionary Biology|Electrical Engineering and Computer Science|MIT OpenCourseWare

## References

1. ↑ "Intel ISEF Categories and Subcategories." *Student Science*. Society for Science & the Public, 2015. Web. 07 June 2015.
Generative model

The **generative model** (also referred to as the **generative probabilistic model**) is a model which defines "a joint distribution *p*(*x*, *c*|*θ*) over both input vectors and class labels".

## See Also

* Discriminative model
* Generative classifier

## References

1. ↑ Bishop, Christopher M., and Julia Lasserre. "Generative or Discriminative? Getting the Best of Both Worlds." *Bayesian Statistics 8: Proceedings of the Eighth Valencia International Meeting: June 2-6, 2006*. Ed. J. M. Bernardo, M. J. Bayarri, J. O. Berger, A. P. Dawid, D. Heckerman, A. F. M. Smith, and M. West. Oxford: Oxford UP, 2007. 3-24. Print.
Familial hypercholesterolemia

**Familial hypercholesterolemia** (sometimes referred to as **familial hypercholesterolaemia**) is an "inherited condition that causes high levels of LDL (low density lipoprotein) cholesterol levels beginning at birth, and heart attacks at an early age".

## External Links

* Familial hyercholesterolemia: MedlinePlus Medical Encyclopedia

## References

1. ↑ "Learning About Familial Hypercholesterolemia." *National Human Genome Research Institute*. National Institutes of Health, 26 Dec. 2013. Web. 11 Sept. 2015.
Forensic genomics

## External Links

* Forensic Genomics | NGS Solutions for Forensic Applications
* Forensic Genomics Consortium Netherlands

## Further Reading

* Wit, Pierre De, Laura Rogers-Bennett, Raphael M. Kudela, and Stephen R. Palumbi. "Forensic Genomics as a Novel Tool for Identifying the Causes of Mass Mortality Events." *Nature Communications* 5 (2014): n. pag. Print.
ExPASy

**ExPASy** (previously the **Expert Protein Analysis System**) is the "SIB Bioinformatics Resource Portal which provides access to scientific databases and software tools (i.e., resources) in different areas of life sciences including proteomics, genomics, phylogeny, systems biology, population genetics, transcriptomics etc".

## References

1. ↑ Artimo P, Jonnalagedda M, Arnold K, Baratin D, Csardi G, de Castro E, Duvaud S, Flegel V, Fortier A, Gasteiger E, Grosdidier A, Hernandez C, Ioannidis V, Kuznetsov D, Liechti R, Moretti S, Mostaguir K, Redaschi N, Rossier G, Xenarios I, and Stockinger H. ExPASy: SIB bioinformatics resource portal, *Nucleic Acids Res*, 40(W1):W597-W603, 2012.
Exhaustive search

**Exhaustive search** (also known as **brute-force search**, **sequential search**, or the **naive shifting algorithm**) is a "search algorithm which traverses all the elements of the given set".

## External Links

* Exhaustive Search -- from Wolfram MathWorld

## References

1. ↑ "Brute Force Algorithms." *Eitan M. Gurari*. Department of Computer Science and Engineering, The Ohio State University, n.d. Web. 11 Oct. 2015.
Contig

A **contig** is a "contiguous set of overlapping DNA sequences".

## References

1. ↑ Brown TA. *Genomes*. 2nd edition. Oxford: Wiley-Liss; 2002. Glossary. Available from: http://www.ncbi.nlm.nih.gov/books/NBK21126/
2. ↑ Izard, Jacques, and Maria C. Rivera, eds. *Metagenomics for Microbiology*. 1st ed. London: Academic, 2014. Print.
Consensus sequence

A **consensus sequence** is "one of the forms of representation of the sequence conservation in an alignment of DNA or protein sequences".

## References

1. ↑ Koonin EV, Galperin MY. *Sequence - Evolution - Function: Computational Approaches in Comparative Genomics*. Boston: Kluwer Academic; 2003. Glossary. Available from: http://www.ncbi.nlm.nih.gov/books/NBK20257/
Cluster analysis

**Cluster analysis** or **clustering** is a "statistical classification technique in which cases, [[data], or objects (events, people, things, etc.) are sub-divided into groups (clusters) such that the items in a cluster are very similar (but not identical) to one another and very different from the items in other clusters. It is a discovery tool that reveals associations, patterns, relationships and structures in masses of data".

## References

1. ↑ "What Is Cluster Analysis?" *BusinessDictionary.com*. WebFinance, Inc., n.d. Web. 9 June 2016.
Eflornithine

**Eflornithine** (**α-difluoromethylornithine** or **DFMO**) is an "inhibitor of the enzyme catalyzing the decarboxylation of ornithine; used topically as the hydrochloride salt to reduce unwanted facial hair in females".

## References

1. ↑ "eflornithine." *Miller-Keane Encyclopedia and Dictionary of Medicine, Nursing, and Allied Health, Seventh Edition*. 2003. Saunders, an imprint of Elsevier, Inc 1 Nov. 2015 <http://medical-dictionary.thefreedictionary.com/eflornithine>
Depth-first search

**Depth-first search** (**DFS**) may refer to a "search algorithm that considers outgoing edges (children) of a vertex before any of the vertex's siblings, that is, outgoing edges of the vertex's predecessor in the search. Extremes are searched first. This is easily implemented with recursion".

**Depth-first search** (**DFS**) may also refer to an "algorithm that marks all vertices in a directed graph in the order they are discovered and finished, partitioning the graph into a forest".

## References

1. ↑ 1.0 1.1 Paul E. Black, "depth-first search", in *Dictionary of Algorithms and Data Structures* [online], Vreda Pieterse and Paul E. Black, eds. 22 April 2015. (accessed 21 Oct. 2015) Available from: http://www.nist.gov/dads/HTML/depthfirst.html
Enzyme regulation

**Enzyme regulation** refers to the "control of the rate of a reaction catalyzed by an enzyme by some effector (for example, inhibitors or activators) or by alteration of some condition (for example, pH or ionic strength)".

## References

1. ↑ "enzyme regulation." *Farlex Partner Medical Dictionary*. 2012. Farlex 1 Nov. 2015 <http://medical-dictionary.thefreedictionary.com/enzyme+regulation>
Domain architecture

The **domain architecture** of a protein is the "sequential order of the domains and their sequence from the N-terminus to the C-terminus (computationally based on existing domain databases, such as Pfam)".

## References

1. ↑ Lin, K., L. Zhu, and D.-Y. Zhang. "An Initial Strategy for Comparing Proteins at the Domain Architecture Level." *Bioinformatics* 22.17 (2006): 2081-086. Print.
Ensembl REST API endpoints

The **Ensembl REST API endpoints** are entry points to the Ensembl REST API service.

## Archive

### GET archive/id/:id

* Description: "Uses the given identifier to return the archived sequence".
* Parameters
	+ Required: "An Ensembl stable ID".
	+ Optional: "Name of the callback subroutine to be returned by the requested JSONP response. Required ONLY when using JSONP as the serialisation method".

### POST archive/id

* Description: "Retrieve the archived sequence for a set of identifiers".

## References

1. ↑ 1.0 1.1 1.2 1.3 "Ensembl Rest API Endpoints." Ensembl REST API (Version 4.2). WTSI & EBI, June 2015. Web. 05 June 2015.
Energy minimization

## External Links

* ENERGY MINIMIZATION
* Energy Minimization

## Further Reading

* Szeliski, Richard, Ramin Zabih, Daniel Scharstein, Olga Veksler, Vladimir Kolmogorov, Aseem Agarwala, Marshall Tappen, and Carsten Rother. "A Comparative Study of Energy Minimization Methods for Markov Random Fields." *Computer Vision – ECCV 2006 Lecture Notes in Computer Science* (2006): 16-29. Print.
Guanidinium

**Guanidinium** refers to a "protonated guanidine moiety in a molecule (for example, in arginine)".

## Further Reading

* Vanzi, Francesco, Bhupinder Madan, and Kim Sharp. "Effect of the Protein Denaturants Urea and Guanidinium on Water Structure: A Structural and Thermodynamic Study." *Journal of the American Chemical Society* 120.41 (1998): 10748-0753. Print.

## References

1. ↑ "guanidinium." *Farlex Partner Medical Dictionary*. 2012. Farlex 28 Sep. 2015 <http://medical-dictionary.thefreedictionary.com/guanidinium>
Greedy algorithm

A **greedy algorithm** is an "algorithm that always takes the best immediate, or local, solution while finding an answer. Greedy algorithms find the overall, or globally, optimal solution for some optimization problems, but may find less-than-optimal solutions for some instances of other problems".

## References

1. ↑ Paul E. Black, "greedy algorithm", in *Dictionary of Algorithms and Data Structures* [online], Vreda Pieterse and Paul E. Black, eds. 2 February 2005. (accessed 12 December 2015) Available from: http://www.nist.gov/dads/HTML/greedyalgo.html
EMBL-EBI services

**EMBL-EBI services** are services offered by the European Bioinformatics Institute.

* 1000 Genomes
* ArrayExpress Archive of Functional Genomics Data
* BioJS
* BioModels database
* CENSOR
* ChEMBL: Bioactive data for drug discovery
* Chemical Entities of Biological Interest
* Clustal Omega
* Clustal Phylogeny
* ClustalW2
* Complex Portal
* DaliLite
* Database of Genomic Variants archive
* DbClustal
* dbfetch
* Distributed Annotation System (sensu protein sequences)
* EBI BioSamples Database
* EBI Metagenomics
* EBI Search
* EMBOSS Tools
* ENA Sequence Search
* ENA/SVA - Sequence Version Archive
* Ensembl
* Ensembl Genomes
* Enzyme Portal: Integrated enzyme data from EMBL-EBI resources
* Europe PubMed Central
* European Genome-phenome Archive
* European Mouse Mutation Archive
* European Nucleotide Archive
* European Variation Archive
* Experimental Factor Ontology
* Expression Atlas
* FASTA [nucleotide]
* FASTA [protein]
* FASTM [nucleotide]
* FASTM [protein]
* FingerPRINTScan
* Gene Ontology
* GeneWise
* GGSEARCH [nucleotide]
* GGSEARCH [protein]
* GGSEARCH [nucleotide]
* GGSEARCH [protein]
* HMMER - protein homology search
* HUGO Gene Nomenclature Committee
* IMGT/HLA
* Infrafrontier-I3
* IntAct Molecular Interaction Database
* Integrated GPCR bioactivity, sequence and structure data
* Integrated Kinase biactivity, sequence and structure data
* IntEnz: Integrated relational enzyme database
* InterPro
* InterProScan 5
* Job Dispatcher
* Kalign
* LALIGN [nucleotide]
* LALIGN [protein]
* MAFFT
* MapMi
* MEROPS
* MetaboLights: Metabolomics archive and reference database
* MUSCLE
* MView
* NCBI BLAST [nucleotide]
* NCBI BLAST [protein]
* NHGRI-EBI GWAS Catalog
* Ontology Lookup Service
* Patent databases
* PDBe EM Resources
* PDBe NMR Resources
* PDBeChem
* PDBeFold
* PDBeMotif
* PDBePISA
* Pfam
* Phobius
* PICR: The Protein Identifier Cross-Reference Service
* PomBase
* Pratt - Pattern Matching
* PRIDE: The Proteomics Identifications Database
* PromoterWise
* PROSITE Scan
* Protein Data Bank in Europe
* PSI-BLAST
* QuickGo
* RADAR
* Reactome pathways database
* Readseq
* Rfam
* Rhea: Enzyme-catalysed reactions
* RNAcentral
* SAPS - Statistical Analysis of Protein Sequences
* Sequence Checksum Generator
* SSEARCH [nucleotide]
* SSEARCH [protein]
* T-Coffee
* Taxonomy services
* The International Mouse Phenotyping Consortium
* TreeFam
* UniChem: Chemical Structure Cross-referencing
* UniProt: The Universal Protein Resource
* UniSave
* VectorBase
* Web Services
* Whatizit
* Wise2DBA - DNA Block Aligner
* WormBase
* WU-BLAST [nucleotide]
* WU-BLAST [protein]
ENA

The **European Nucleotide Archive** (**ENA**) is a tool which "provides a comprehensive record of the world's nucleotide sequencing information, covering raw sequencing data, sequence assembly information and functional annotation".

## References

1. ↑ "European Nucleotide Archive." *EMBL-EBI*. EMBL-EBI, n.d. Web. 20 July 2015.
Consensus gene sequence

A **consensus gene sequence** is a "sequence that is conserved and may be found multiple times in a genome and also in other species. Consensus sequences show a common function between species. The sequence can show some minor variability but will have some core unchanging residues. A consensus sequence is obtained by aligning the results of multiple sequences from a particular site and identifying the sequence that represents the most commonly found nucleotides at each position".

## References

1. ↑ "EMBLog Bioinformatics Glossary." *EMBLog*. EMBLog, 2013. Web. 21 July 2015.
Epigenome

The **epigenome** is the "complete set of epigenetic modifications, which are heritable or transitory changes in phenotype or gene expression that result from mechanisms other than changes in the DNA sequence in a given individual, tissue, tumor, or population".

## References

1. ↑ Committee on the Review of Omics-Based Tests for Predicting Patient Outcomes in Clinical Trials; Board on Health Care Services; Board on Health Sciences Policy; Institute of Medicine; Micheel CM, Nass SJ, Omenn GS, editors. *Evolution of Translational Omics: Lessons Learned and the Path Forward*. Washington (DC): National Academies Press (US); 2012 Mar 23. Glossary. Available from: http://www.ncbi.nlm.nih.gov/books/NBK202162/
HHsenser

**HHsenser** is a "sensitive intermediate profile search using HMM-HMM comparison. HHsenser takes a sequence or an alignment as input and builds an alignment with as many near or remote homologs as possible. It uses representative sequences in the vicinity of the input alignment as seeds to build new alignments with PSI-BLAST".

## Further Reading

* Söding, Johannes et al. "HHsenser: Exhaustive Transitive Profile Search Using HMM–HMM Comparison." *Nucleic Acids Research* 34.Web Server issue (2006): W374–W378. *PMC*. Web. 9 June 2015.

## References

1. ↑ "Search Tools." *Bioinformatics Toolkit*. Department of Protein Evolution at the Max Planck Institute for Developmental Biology, Tübingen, 2015. Web. 09 June 2015.
FASTQ format

## See Also

* Sanger FASTQ format
* Solexa FASTQ format
* Illumina 1.3+ FASTQ format
* ABI SOLiD Colour Space FASTQ format

## Further Reading

* Cock, P. J. A., C. J. Fields, N. Goto, M. L. Heuer, and P. M. Rice. "The Sanger FASTQ File Format for Sequences with Quality Scores, and the Solexa/Illumina FASTQ Variants." *Nucleic Acids Research* 38.6 (2009): 1767-771. Print.
Exaptation

**Exaptation** is the "recruitment of a protein for a new function, which may be mechanistically but not biologically related to the original one".

## References

1. ↑ Koonin EV, Galperin MY. *Sequence - Evolution - Function: Computational Approaches in Comparative Genomics*. Boston: Kluwer Academic; 2003. Glossary. Available from: http://www.ncbi.nlm.nih.gov/books/NBK20257/
Database

A **database** (**DB**) is a "set of data that has a regular structure and that is organized in such a way that a computer can easily find the desired information".

## References

1. ↑ "Database Definition." *The Linux Information Project (LINFO)*. The Linux Information Project, 22 June 2006. Web. 06 June 2015.
2. ↑ "What Is Database (DB)?" *Webopedia*. QuinStreet Inc., 2015. Web. 06 June 2015.
Dynamic programming

**Dynamic programming** refers to the technique by which one can "solve an optimization problem by caching subproblem solutions (memoization) rather than recomputing them".

## References

1. ↑ Algorithms and Theory of Computation Handbook, CRC Press LLC, 1999, "dynamic programming", in *Dictionary of Algorithms and Data Structures* [online], Vreda Pieterse and Paul E. Black, eds. 23 March 2015. (accessed 12 December 2015) Available from: http://www.nist.gov/dads/HTML/dynamicprog.html
Computational biology

**Computational biology** is the "development and application of data-analytical and theoretical methods, mathematical modeling and computational simulation techniques
to the study of biological, behavioral, and social systems".

## References

1. ↑ "NIH WORKING DEFINITION OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY." *Biomedical Information Science & Technology Initiative*. National Institutes of Health, 17 July 2000. Web. 12 June 2015.
DNA sequence

A **DNA sequence** (also called a **nucleotide sequence**, **nucleic acid sequence**, or **base sequence**) is the "sequence of purines and pyrimidines in nucleic acids and polynucleotides".

## References

1. ↑ "Base Sequence - Glossary Entry." *Genetics Home Reference*. Health On the Net Foundation, 12 June 2015. Web. 05 June 2015.
Compression

In computing and computer science, **compression** (sometimes referred to as **data compression**, **source coding**, or **bit-rate reduction**) refers to the storage of data in a format which requires less space than usual.

## References

1. ↑ Beal, Vangie. "What Is Data Compression?" *Webopedia*. QuinStreet Inc., n.d. Web. 12 Oct. 2015.
Drug utilization research

**Drug utilization research** refers to the "marketing, distribution, prescription, and use of drugs in a society, with special emphasis on the resulting medical, social and economic consequences".

## References

1. ↑ "Introduction to Drug Utilization Research: Chapter 1: What Is Drug Utilization Research and Why Is It Needed?: 1.1. Definition and Domains." *Essential Medicines and Health Products Information Portal*. WHO, 30 July 2015. Web. 02 Oct. 2015.
Channelopathy

**Channelopathy** is a "popular term for a heterogeneous group of conditions caused by structural (due to mutations) or functional (acquired, e.g., autoimmune) defects in ion channels or their regulatory proteins".

## Further Reading

* Kass, Robert S. “The Channelopathies: Novel Insights into Molecular and Genetic Mechanisms of Human Disease.” *Journal of Clinical Investigation* 115.8 (2005): 1986–1989. PMC. Web. 17 Dec. 2015.

## References

1. ↑ "channelopathy." *Segen's Medical Dictionary*. 2011. Farlex, Inc. 17 Dec. 2015 <http://medical-dictionary.thefreedictionary.com/channelopathy>
Guake

**Guake** is a "top-down terminal for Gnome (in the style of Yakuake for KDE, Tilda or the terminal used in Quake)".

## External Links

* Guake/guake at GitHub
* Guake › Wiki › ubuntuusers.de
* Guake - ArchWiki
* Guake Terminal - Ubuntu Apps Directory

## References

1. ↑ "Guake Terminal - What Is It?" *Guake Terminal*. N.p., n.d. Web. 10 June 2015.
Chymotrypsinogen

**Chymotrypsinogen** is the "inactive precursor of chymotrypsin, the form in which it is secreted by the pancreas".

## References

1. ↑ "chymotrypsinogen." *Miller-Keane Encyclopedia and Dictionary of Medicine, Nursing, and Allied Health, Seventh Edition*. 2003. Saunders, an imprint of Elsevier, Inc 1 Nov. 2015 <http://medical-dictionary.thefreedictionary.com/chymotrypsinogen>
Classical genetics

**Classical genetics** is a branch of genetics "concerned primarily with the method by which genetic traits ... are transmitted in plants and animals.

## References

1. ↑ "genetics". *Encyclopædia Britannica*. *Encyclopædia Britannica Online*. Encyclopædia Britannica Inc., 2015. Web. 25 Jun. 2015 <http://www.britannica.com/science/genetics/DNA-and-the-genetic-code>.
Convolution

A **convolution** is an "an integral that expresses the amount of overlap of one function *g* as it is shifted over another function *f*. It therefore 'blends' one function with another".

## See Also

* Autocorrelation
* Cauchy product
* Convolution theorem
* Cross-correlation
* Recurrence plot
* Wiener-Khinchin theorem

## References

1. ↑ Weisstein, Eric W. "Convolution." From *MathWorld*--A Wolfram Web Resource. http://mathworld.wolfram.com/Convolution.html
EU-ADR project

**EU-ADR project** is an effort to "exploit different European electronic healthcare records (EHR) databases for drug safety signal detection".

## References

1. ↑ Trifiro, G., A. Fourrier-Reglat, M. C. Sturkenboom, C. Díaz Acedo, J. Van Der Lei, and EU-ADR Group. "The EU-ADR Project: Preliminary Results and Perspective." *Studies in Health Technology and Informatics* 148 (2009): 43-49. Print.
Dijkstra's algorithm

**Dijkstra's algorithm** is an "algorithm to find the shortest paths from a single source vertex to all other vertices in a weighted, directed graph. All weights must be nonnegative".

## External Links

* Dijkstra's algorithm in 3 minutes - Review and example - YouTube
* Dijkstra's Algorithm for Shortest Route Problems

## References

1. ↑ Paul E. Black, "Dijkstra's algorithm", in *Dictionary of Algorithms and Data Structures* [online], Vreda Pieterse and Paul E. Black, eds. 20 September 2006. (accessed 15 November 2015) Available from: http://www.nist.gov/dads/HTML/dijkstraalgo.html
Genetic counseling

**Genetic counseling** is a "process, involving an individual or family, comprising: evaluation to confirm, diagnose, or exclude a genetic condition, malformation syndrome, or isolated birth defect; discussion of natural history and the role of heredity; identification of medical management issues; calculation and communication of genetic risks; provision of or referral for psychosocial support".

## References

1. ↑ Pagon RA, Adam MP, Ardinger HH, et al., editors. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2015. *Illustrated Glossary*. Available from: http://www.ncbi.nlm.nih.gov/books/NBK5191/
Consultand

A **consultand** is an "individual (not necessarily affected) who presents for genetic counseling and through whom a family with an inherited disorder comes to medical attention".

## References

1. ↑ Pagon RA, Adam MP, Ardinger HH, et al., editors. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2015. *Illustrated Glossary*. Available from: http://www.ncbi.nlm.nih.gov/books/NBK5191/
GI number

A **GI number** (sometimes written in lower case, "**gi**") is "simply a series of digits that are assigned consecutively to each sequence record processed by NCBI. The GI number bears no resemblance to the Accession number of the sequence record".

## References

1. ↑ "Sequence Identifiers: A Historical Note." *NCBI*. U.S. National Library of Medicine, 14 June 2004. Web. 10 Aug. 2015.
Deterministic algorithm

A **deterministic algorithm** is an "algorithm whose behavior can be completely predicted from the input".

## References

1. ↑ Paul E. Black, "deterministic algorithm", in *Dictionary of Algorithms and Data Structures* [online], Vreda Pieterse and Paul E. Black, eds. 14 January 2009. (accessed 13 December 2015) Available from: http://www.nist.gov/dads/HTML/deterministicAlgorithm.html
Clustering

In computer science, **clustering** refers to the "tendency for entries in a hash table using open addressing to be stored together, even when the table has ample empty space to spread them out". It may also refer to "connecting two or more computers together in such a way that they behave like a single computer", (this is occasionally referred to as **computer clustering**). Further, **clustering** may refer to cluster analysis, graph clustering, or data clustering.

## References

1. ↑ Paul E. Black, "clustering", in *Dictionary of Algorithms and Data Structures* [online], Vreda Pieterse and Paul E. Black, eds. 30 December 2005. (accessed TODAY) Available from: http://www.nist.gov/dads/HTML/clustering.html
2. ↑ Beal, Vangie. "Clustering." *Webopedia*. Quinstreet Enterprise, n.d. Web. 9 June 2016.
DELTA-BLAST

**Domain Enhanced Lookup Time Accelerated BLAST** (**DELTA-BLAST**) is an algorithm which "searches a database of pre-constructed PSSMs before searching a protein-sequence database, to yield better homology detection. For its PSSMs, DELTA-BLAST employs a subset of NCBI's Conserved Domain Database (CDD)".

## References

1. ↑ Boratyn, Grzegorz M et al. "Domain Enhanced Lookup Time Accelerated BLAST." *Biology Direct* 7 (2012): 12. *PMC*. Web. 17 June 2015.
DsDNA

**dsDNA** (**double-stranded DNA**) refers to a "molecule of DNA consisting of two parallel strands joined by hydrogen bonds between complementary purines and pyrimidines; a double helix, the form in which DNA occurs in chromosomes".

## References

1. ↑ "double-stranded DNA." *Farlex Partner Medical Dictionary*. 2012. Farlex 23 Oct. 2015 <http://medical-dictionary.thefreedictionary.com/double-stranded+DNA>
Connected component

A **connected component** is one of a set of maximally connected components of an unidirected graph.

## References

1. ↑ Alen Lovrencic, "connected components", in *Dictionary of Algorithms and Data Structures* [online], Vreda Pieterse and Paul E. Black, eds. 2 September 2014. (accessed 21 Oct. 2015) Available from: http://www.nist.gov/dads/HTML/connectedComponents.html
Gibbs energy

**Gibbs energy** (also referred to as **Gibbs free energy**, **Gibbs function**, or **free enthalpy**) is "enthalpy minus the product of thermodynamic temperature and entropy".

## References

1. ↑ IUPAC. Compendium of Chemical Terminology, 2nd ed. (the "Gold Book"). Compiled by A. D. McNaught and A. Wilkinson. Blackwell Scientific Publications, Oxford (1997). XML on-line corrected version: http://goldbook.iupac.org (2006-) created by M. Nic, J. Jirat, B. Kosata; updates compiled by A. Jenkins. ISBN 0-9678550-9-8. doi:10.1351/goldbook.
Conserved substitution

A **conserved substitution** is a "change at a specific position of an amino acid or, less commonly, DNA sequence that preserves the physico-chemical properties of the original residue or achieves a positive score in the governing scoring matrix".

## References

1. ↑ Fassler J, Cooper P. *BLAST Glossary*. 2011 Jul 14. In: BLAST® Help [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2008-. Available from: http://www.ncbi.nlm.nih.gov/books/NBK62051/
Horner's method

**Horner's method** (also known as **Horner's method of approximation**, **Horner's rule**, **Horner's scheme**, or **Horner's rule for polynomial evaluation**) is a "standard minimum arithmetic method for evaluating and
deflating polynomials. It can also efficiently evaluate various order derivatives of a polynomial, therefore is often used as part of Newton’s method".

## External Links

* Horner's Method -- from Wolfram MathWorld

## References

1. ↑ Burrus, C. Sidney, James W. Fox, Gary A. Sitton, and Sven Treital. "Horner's Method for Evaluating and Deflating Polynomials." *DSP Software*. Rice University, 26 Nov. 2003. Web. 11 Oct. 2015.
Markov chain Monte Carlo

**Markov chain Monte Carlo** (**MCMC**) is a "general purpose technique for generating fair samples from a probability in high-dimensional space, using random numbers drawn from uniform probability in certain range".

## See Also

* Gibbs sampler
* Markov chain
* Markov property
* Metropolis algorithm
* Metropolis-Hastings algorithm
* Metropolis-Hastings-Green algorithm
* Monte Carlo integration
* Ordinary Monte Carlo
* Strong law of large numbers

## References

1. ↑ Zhu, Song-Chun, Frank Dellaert, and Zhuowen Tu. "Markov Chain Monte Carlo for Computer Vision." *Center for Vision, Cognition, Learning, and Autonomy (VCLA)*. Center for Vision, Cognition, Learning, and Autonomy, Oct. 2005. Web. 9 June 2016.
Chirality

**Chirality** is the "geometric property of a rigid object (or spatial arrangement of points or atoms) of being non-superposable on its mirror image; such an object has no symmetry elements of the second kind (a mirror plane, *σ* = *S*1, a [center] of inversion, *i* = *S*2, a rotation-reflection axis, *S*2n)".

## References

1. ↑ IUPAC. Compendium of Chemical Terminology, 2nd ed. (the "Gold Book"). Compiled by A. D. McNaught and A. Wilkinson. Blackwell Scientific Publications, Oxford (1997). XML on-line corrected version: http://goldbook.iupac.org (2006-) created by M. Nic, J. Jirat, B. Kosata; updates compiled by A. Jenkins. ISBN 0-9678550-9-8. doi:10.1351/goldbook.
DNA template

A **DNA template** (also referred to as **template DNA** or sometimes simply as a **template**) is "one strand of DNA that directs synthesis of a complementary DNA strand during DNA replication or of an RNA during transcription".

## References

1. ↑ Lodish H, Berk A, Zipursky SL, et al. *Molecular Cell Biology*. 4th edition. New York: W. H. Freeman; 2000. Glossary. Available from: http://www.ncbi.nlm.nih.gov/books/NBK21607/
De novo mutation

A **de novo mutation** (also referred to as a **de novo gene mutation**, **new gene mutation**, or **new mutation**) is an "alteration in a gene that is present for the first time in one family member as a result of a mutation in a germ cell (egg or sperm) of one of the parents or in the fertilized egg itself".

## References

1. ↑ "De Novo Mutation - Glossary Entry." *Genetics Home Reference*. National Institutes of Health, 19 July 2015. Web. 23 July 2015.
Competitive inhibition

**Competitive inhibition** refers to the "inhibition of enzyme activity by an inhibitor (a substrate analogue) that competes with the substrate for binding sites on the enzymes".

## References

1. ↑ "competitive inhibition." *Miller-Keane Encyclopedia and Dictionary of Medicine, Nursing, and Allied Health, Seventh Edition*. 2003. Saunders, an imprint of Elsevier, Inc 1 Nov. 2015 <http://medical-dictionary.thefreedictionary.com/competitive+inhibition>
Gene

A **gene** is a "genomic sequence (DNA or RNA) directly encoding functional product molecules, either RNA or protein".

## References

1. ↑ Mark B. Gerstein, Can Bruce, Joel S. Rozowsky, Deyou Zheng, Jiang Du, Jan O. Korbel, Olof Emanuelsson, Zhengdong D. Zhang, Sherman Weissman, and Michael Snyder. "What is a gene, post-ENCODE? History and updated definition." *Genome Res*. June 2007 17: 669-681.
Convergent evolution

**Convergent evolution** is the "process by which organisms, taxa, or other biological units (e.g., genes or proteins) that are not derived from a common ancestor have independently acquired comparable (analogous) traits. Convergent evolution can be the result of adapting to, e.g., the same ecological niche, or can be the result of other selective pressures".

## References

1. ↑ "EMBLog Bioinformatics Glossary." *EMBLog*. EMBLog, 2013. Web. 21 July 2015.
GroES/GroEL

## External Links

* Figure 3: The GroEL-GroES reaction cycle.
* Figure 3: Folding in the GroEL–GroES chaperonin cage.
* GroEL Folding Mechanism - CHEM645 Protein Structure and Function

## Further Reading

* Keskin, O., I. Bahar, D. Flatow, D. G. Covell, and R. L. Jernigan. "Molecular Mechanisms of Chaperonin GroEL−GroES Function." *Biochemistry* 41.2 (2002): 491-501. Print.
Genotyping

**Genotyping** refers to the "testing that reveals the specific alleles inherited by an individual; particularly useful for situations in which more than one genotypic combination can produce the same clinical presentation, as in the ABO blood group, where both the AO and AA genotypes yield type A blood".

## References

1. ↑ Pagon RA, Adam MP, Ardinger HH, et al., editors. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2015. *Illustrated Glossary*. Available from: http://www.ncbi.nlm.nih.gov/books/NBK5191/
Deep neural network

A **deep neural network** (**DNN**; also referred to as a **deep-learning network**) is an architecture which contains an input layer and an output layer, separated by *l* layers of hidden units.

## External Links

* Introduction to Deep Neural Networks - Deeplearning4j: Open-source, distributed deep learning for the JVM

## References

1. ↑ Larochelle, Hugo, Yoshua Bengio, Jérôme Louradour, and Pascal Lamblin. "Exploring Strategies for Training Deep Neural Networks." *Journal of Machine Learning Research* 1 (2009): 1-40. Print.
Genomics and Computational Biology

***Genomics and Computational Biology*** is an MIT OpenCourseWare course which assesses the "relationships among sequence, structure, and function in complex biological networks as well as progress in realistic modeling of quantitative, comprehensive, functional genomics analyses. Exercises ... include algorithmic, statistical, database, and simulation approaches and practical applications to medicine, biotechnology, drug discovery, and genetic engineering. Future opportunities and current limitations [are also] critically addressed. In addition to the regular lecture sessions, supplementary sections are scheduled to address issues related to Perl, Mathematica and biology".

## References

1. ↑ "Genomics and Computational Biology." MIT OpenCourseWare. Massachusetts Institute of Technology, n.d. Web. 07 June 2015.
Continue

**continue** refers to a function or statement within several different programming languages.

C

### GCC

"The continue statement in loops .can. to terminate an iteration of the loop and begin the next iteration ... a continue statement inside a loop which itself is inside a loop, then it affects only the innermost loop."

## Java

### Java SE 8

"The continue statement skips the current iteration of a for, while , or do-while loop. The unlabeled form skips to the end of the innermost loop's body and evaluates the boolean expression that controls the loop".

## Perl

### Perl 5 version 20.1

"When followed by a BLOCK, continue is actually a flow control statement rather than a function. If there is a continue BLOCK attached to a BLOCK (typically in a while or foreach), it is always executed just before the conditional is about to be evaluated again, just like the third part of a for loop in C. Thus it can be used to increment a loop variable, even when the loop has been continued via the next statement (which is similar to the C continue statement)".

## References

1. ↑ O'Riordan, Ciaran. "The Continue Statement." *The GNU C Reference Manual*. Free Software Foundation, Inc., 2002. Web. 07 June 2015.
2. ↑ "Branching Statements." *The Java Tutorials*. Oracle, 2015. Web. 07 June 2015.
3. ↑ Allen, Jon. "Continue." *Perldoc.perl.org*. N.p., n.d. Web. 07 June 2015.
Microtubule-associated protein

A **microtubule-associated protein** (**MAP**) is "any protein, including motor proteins, that binds to microtubules in a constant ratio and determines the unique properties of different types of microtubules".

## References

1. ↑ Lodish H, Berk A, Zipursky SL, et al. *Molecular Cell Biology*. 4th edition. New York: W. H. Freeman; 2000. Glossary. Available from: http://www.ncbi.nlm.nih.gov/books/NBK21607/
Collision

A **collision** (shortened from **hash collision** or **hashing collision**; also referred to as a "**hash clash**") refers to "when two different keys hash to the same value, i.e. to the same location in a hash table".

## References

1. ↑ "hash collision." *The Free On-line Dictionary of Computing*. 2003. Denis Howe 10 Oct. 2015 <http://encyclopedia2.thefreedictionary.com/hash+collision>
EOL API

The **EOL API** is an API which allows access to the "functionality of EOL into your own website and tools, helping to make EOL an ingredient in biodiversity applications".

## References

1. ↑ "EOL Application Programming Interface (API) Overview - Encyclopedia of Life." *Encyclopedia of Life*. N.p., n.d. Web. 06 June 2015.
Lpwd

**lpwd** (also sometimes stylized as **LPWD** or **LPwd**) is a command or subcommand.

## PSFTP

lpwd "display[s] your current local working directory".

## WinSCP

lpwd "prints current local working directory (valid for all sessions)".

## External Links

* IBM Knowledge Center|LPwd subcommand—Display the current working-level qualifier

## References

1. ↑ "6.2.8 The Lcd and Lpwd Commands: Changing the Local Working Directory." *Helpdoc-online / PuTTY 0.6*. N.p., n.d. Web. 15 June 2015.
2. ↑ "Lpwd." *WinSCP*. Black Gate Publishing, 25 Apr. 2014. Web. 15 June 2015.
Hmmpfam

**hmmpfam** (often stylized as **HMMPFAM** or **HmmPfam** and sometimes referred to as **HMMERPFAM** or **HmmerPfam**) is a "part of the HMMer package" which "compares one or more sequences to a database of profile hidden Markov models, such as the Pfam library, in order to identify known domains within the sequences".

## External Links

* hmmpfam - search a single sequence against an HMM database

## References

1. ↑ "Hmmpfam." *Bio-Linux Software Documentation Project*. NERC Environmental Bioinformatics Centre, n.d. Web. 24 June 2015.
2. ↑ "HMMERPFAM." *HmmerPfam*. Accelrys Inc., 9 Jan. 2002. Web. 24 June 2015.
Hamiltonian cycle

A **Hamiltonian cycle** (also referred to as a **Hamiltonian circuit** is a "path through a graph that starts and ends at the same vertex and includes every other vertex exactly once".

## References

1. ↑ Paul E. Black, "Hamiltonian cycle", in *Dictionary of Algorithms and Data Structures* [online], Vreda Pieterse and Paul E. Black, eds. 2 September 2014. (accessed 13 December 2015) Available from: http://www.nist.gov/dads/HTML/hamiltonianCycle.html