recursal/Fanatic-Fandom huggingface dataset:
2015 NAR Database Summary Paper Alphabetic List

The **2015 NAR Database Summary Paper Alphabetic List** is a list of databases included in the publication *Nucleic Acids Research*.

1

* 1000 Genomes Selection Browser
* 16S and 23S Ribosomal RNA Mutation Database

2

* 2D-PAGE
* 2P2Idb
* 3D rRNA modification maps

3

* 3D-Footprint
* 3D-Genomics
* 3D-Interologs
* 3DID - 3D interacting domains
* 3DNALandscapes
* 3DSwap: Database of Proteins involved in 3D domain Swapping

4

* 4DXpress

5

* 5S Ribosomal RNA Database

A

* AAindex
* AANT - Amino Acid - Nucleotide interaction database (discontinued)
* ABA - Ascidian Body Atlas
* ABCdb
* ABS
* ACeDB
* ACLAME - A Classification of Mobile genetic Elements
* ACTIVITY
* ADDA - A Domain Database
* Addgene Repository Database
* ADHDgene
* ADReCS
* AffinDB
* AgBase
* AGD - *Ashbya* Genome Database
* AgeFactDB
* AGRIS - *Arabidopsis* Gene Regulatory Information Server
* AHTPdb
* ALFRED
* Allele Frequency Net
* Allen Brain Atlas
* Allosteric Database
* ALPSbase
* AlterORF
* AlzGene
* Aminoacyl-tRNA synthetase database
* AmoebaDB
* Androgen Receptor Gene Mutations Database
* Animal Genome Size Database
* Animal Toxin Database
* AnimalQTLdb
* AnimalTFDB
* AntigenDB
* AntiJen
* APASdb
* APD - Antimicrobial Peptide Database
* AphidBase
* ApiDB - Apicomplexan DataBase
* ApiDots
* ApoHoloDB
* AppaDB
* APPRIS
* Aptamer Database
* Arabidopsis Hormone Database
* Arabidopsis Mitochondrial Protein Database
* Arabidopsis MPSS
* Arabidopsis Nucleolar Protein Database
* ArachnoSever
* ARAMEMNON
* AraNet
* Araport
* ArchDB
* ARDB
* ARED
* AREsite
* ArkDB
* ArrayExpress
* ArrayMap
* ARTADEdb
* AS-ALPS
* ASAP - A Systematic Annotation Package
* ASAP II
* ASC - Active Sequence Collection
* ASPD
* Aspergillus Genomes
* AspGD
* ASPicDB
* ASRP - Arabidopsis Small RNA Project
* ASTD
* ATGC
* AtGDB
* AthaMap
* Atlas of Genetics and Cytogenetics in Oncology and Haematology
* AtPID
* ATTED-II
* AutDB
* AutismKB
* Autophagy Database
* AutoPSI
* autoSNPdb
* AVPdb

## External Links

* Oxford Journals | Life Sciences | Nucleic Acids Research | Database Summary Paper Alpha List
Epigenomics

**Epigenomics** is the "study of epigenetic modifications across the whole genome".

## Further Reading

* Callinan, P. A. "The Emerging Science of Epigenomics." *Human Molecular Genetics* 15.Suppl 1 (2006): R95-101. Print.

## References

1. ↑ "EPIGENOMICS." *Biology 309: Genomics, Proteomics and Systems Biology*. Davidson College, 2014. Web. 08 June 2015.
All Stars 1

A primeira temporada não-tradicional do RuPaul's Paper Race, o All Stars: Heroes vs. Villains (All Stars 1) foi confirmada para novembro em agosto de 2015. Pela primeira vez, as queens foram selecionadas em sigilo, e divulgadas mais de um mês depois, recebendo uma lista de Runways e Lipsyncs para fazerem antes da temporada começar. Em setembro, foi lançada uma imagem para o público descobrir os Lipsyncs da temporada. Em 7 de outubro, após o 15 Fan Favorite Queens Of All Time, foram divulgadas as fotos promocionais da apresentadora Ruzy Q, e além das fotos, também foi revelado que além de juradas, Ally Lavire e Bárbara Boom seriam mentoras do Team Heroes e Isabelle Époque e Sartana mentoras do Team Villains. Em 8 de outubro foi divulgado um vídeo com sombras misteriosas das 14 participantes.

As 14 queens foram reveladas em 8 e 9 de outubro. O Red Carpet da Premiere aconteceu dia 26 de outubro, uma série de posts especiais foram feitos até dia o 1º de novembro (o dia que as queens entraram na Workroom) incluindo Drag Tips, Fan Arts feitas por Ira D'Essance, anúncio da primeira temporada do Watcha Packin', um vídeo com dicas dos desafios e runways e um vídeo promocional da temporada.

A primeira Runway aconteceu dia 8 de novembro, e nos dois primeiros episódios a dinâmica da temporada foi diferente do habitual: a vencedora do episódio salvaria todas as competidoras do seu grupo (Heroes ou Villains). Mas a partir do terceiro episódio, a competição voltou a ser individual. Após o sexto episódio em dezembro de 2015, houve uma pausa na competição retornando apenas no final de janeiro. Entre o período, ocorreu o Fast Episode da Season 4. Com 11 episódios, a temporada acabou em 6 de março de 2016, com a coroação da Vallentina Versace.

* A Ruzy Q pela primeira vez foi desenhada pela Ira D'Essance.
* Pela primeira vez, em alguns episódios a Ruzy Q não foi Herbertt Cabral e sim Ira D'Essance.
* Única temporada com dois Balls como desafios principais.
* Além da Season 2, é a única temporada a ter mais de dez episódios.

## Competidoras

█ A competidora faz parte da equipe das heroínas.
█ A competidora faz parte da equipe das vilãs.
* Posteriormente foi descoberto que Dory Scooby-Doo era na verdade Isabelle Époque nesta temporada.
* Toxic Fleur é a única participante da história da competição a competir em três temporadas diferentes.

## Progresso das Competidoras

* Fancie Günz foi eliminada por Lipsync no sexto episódio, retornando no oitavo e desistindo no nono.
* Além do Top 3, apenas Made IN Line foi eliminada sem desistir.

## Lipsyncs

█ A competidora foi eliminada no seu primeiro Lipsync.

\* A queen foi para a dublagem e não apresentou look de Lipsync.

## Guest Judges

* André Pessôa (Season 4) - Episódio 3
* Shoshanna Conda - Episódio 6
* Bettie Queen - Episódio 7
* Granada (Season 4) - Episódio 8
* Jhayceen Storm (Season 3) - Episódio 8
* Made IN Line (Season 1) - Episódios 9 e 10

## Episódios

Lista de Episódios do All Stars 1

**\***O episódio ocorreu após o Fast Episode da Season 4.
HHblits

**HHblits** is a "remote homology detection method based on iterative HMM-HMM comparison. HHblits can build high-quality MSAs starting from single sequences or from MSAs. It transforms these into a query HMM and iteratively searches through uniprot20 or nr20 databases by adding significantly similar sequences from the previous search to the updated query HMM for the next search iteration. Compared to PSI-BLAST, HHblits is faster, up to twice as sensitive and produces more accurate alignments".

## References

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

**Fluorescence Resonance Energy Transfer** (**FRET**; also referred to as **Förster resonance energy transfer**) is the "transfer of energy between two fluorophores, and is used to detect the interaction of two labelled molecules in close proximity".

## External Links

* Fluorescence Resonance Energy Transfer - ChemWiki

## References

1. ↑ "Fluorescence Resonance Energy Transfer." *Nature.com*. Nature Publishing Group, n.d. Web. 11 Oct. 2015.
Genetic algorithm

A **genetic algorithm** (**GA**) is an "optimization algorithm based on the mechanisms of Darwinian evolution which uses random mutation, crossover and selection procedures to breed better models or solutions from an originally random starting population or sample".

## 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.
Enzyme

An **enzyme** is a macromolecule, mostly of protein nature, that functions as a catalyst by increasing reaction rate. "In general, an enzyme catalyses only one reaction type (reaction specificity) and operates on only one type of substrate (substrate specificity). Substrate molecules are attacked at the same site (regiospecificity) and only one or preferentially one of the enantiomers of chiral substrates or of racemic mixtures is attacked (stereospecificity)".

## References

1. ↑ *IUPAC Gold Book*. Version 2.3.3. ed. S.l.: IUPAC, 2014. Web.
Computational functional genomics

**Computational functional genomics** is the "study and discussion of computational approaches and algorithms for contemporary problems in functional genomics".

## External Links

* Computational Functional Genomics|Biology|MIT OpenCourseWare

## References

1. ↑ Gifford, David, and Richard Young. "Handout 1 - 6.892/7.90 Computational Functional Genomics." *Gifford Lab*. MIT, 5 Feb. 2002. Web. 7 June 2015.
FASTA format

**FASTA format** (sometimes **FASTA sequence format** or **Pearson format**) is a "text-based format for representing either nucleotide sequences or peptide sequences, in which base pairs or amino acids are represented using single-letter codes. A sequence in FASTA format begins with a single-line description, followed by lines of sequence data. The description line is distinguished from the sequence data by a greater-than (">") symbol in the first column. It is recommended that all lines of text be shorter than 80 characters in length".

## References

1. ↑ "What Is FASTA Format?" *Zhang Lab*. The Regents of the University of Michigan, n.d. Web. 06 June 2015.
Ensembl Project

The **Ensembl Project** is a "joint project between European Bioinformatics Institute (EBI), an outstation of the European Molecular Biology Laboratory (EMBL), and the Wellcome Trust Sanger Institute (WTSI)".

## References

1. ↑ "About the Ensembl Project." *Ensembl release 80*. WTSI / EBI, May 2015. Web. 05 June 2015.
Chromatogram

**Chromatogram** may refer to either the "pattern formed on an adsorbent medium by the layers of components separated by chromatography" and a "time-based graphic record (as of concentration of eluted materials) of a chromatographic separation".

## External Links

* Chromatography - The Chromatogram
* Interpretation of Sequencing Chromatograms

## References

1. ↑ "Chromatogram." *Merriam-Webster*. Merriam-Webster, Incorporated, 2015. Web. 22 Sept. 2015.
GenBank

**GenBank** is a "comprehensive database that contains publicly available nucleotide sequences for more than 240,000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects".

## References

1. ↑ Benson, Dennis A., Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, and David L. Wheeler. "GenBank." *Nucleic Acids Research* 35.Issue Suppl 1 (2007): D21-25. Print.
Digital search tree

A **digital search tree** (**DST**) is a "trie which stores the strings in internal nodes, so there is no need for extra leaf nodes to store the strings".

## References

1. ↑ Paul E. Black, "digital search tree", in *Dictionary of Algorithms and Data Structures* [online], Vreda Pieterse and Paul E. Black, eds. 17 December 2004. (accessed 16 Oct. 2015) Available from: http://www.nist.gov/dads/HTML/digitalSearchTree.html
Faraday cage

A **Faraday cage** or **Faraday shield** is an "enclosure constructed of grounded wire mesh or parallel wires that shields sensitive electrical instruments from electrostatic interference".

## References

1. ↑ "faraday-cage". *Dictionary.com Unabridged*. Random House, Inc. 17 Dec. 2015. <Dictionary.com http://dictionary.reference.com/browse/faraday-cage>.
Gaussian RBM

A **Gaussian restricted Boltzmann machine** (**Gaussian RBM** or **GRBM**) is a restricted Boltzmann machine that is "defined such that the conditional distribution of the visible layer given the hidden layer is a fixed covariance Gaussian with the conditional mean parametrized by the product of a weight matrix and a binary hidden vector".

## References

1. ↑ Courville, Aaron, James Bergstra, and Yoshua Bengio. "A Spike and Slab Restricted Boltzmann Machine." *Journal of Machine Learning Research* 15 (2010): 233-41. Print.
Chymotrypsin

**Chymotrypsin** is a "pancreatic digestive enzyme that catalyzes the hydrolysis of certain proteins in the small intestine into polypeptides and amino acids".

## References

1. ↑ "chymotrypsin." *American Heritage Dictionary of the English Language, Fifth Edition*. 2011. Houghton Mifflin Harcourt Publishing Company 1 Nov. 2015 <http://www.thefreedictionary.com/chymotrypsin>
HHpred

**HHpred** is a "fast server for remote protein homology detection and structure prediction and is the first to implement pairwise comparison of profile hidden Markov models (HMMs)".

It provides "sensitive protein homology detection and structure prediction by HMM-HMM-comparison. Starting from a query sequence, HHpred builds a multiple sequence alignment using HHblits and turns it into a profile HMM. This is then compared it with a database of HMMs representing proteins with known structure (e.g. PDB, SCOP) or annotated protein families (e.g. PFAM, SMART, CDD, COGs, KOGs). The output is a list of closest homologs with alignments. HHpred can also build 3d homology models using the identified templates in the PDB database. It can optimize template picking and query-template alignments for homology modeling".

## References

1. ↑ Söding, Johannes, Andreas Biegert, and Andrei N. Lupas. "The HHpred Interactive Server for Protein Homology Detection and Structure Prediction." *Nucleic Acids Research* 33.Web Server issue (2005): W244–W248. PMC. Web. 5 June 2015.
2. ↑ "Search Tools." *Bioinformatics Toolkit*. Department of Protein Evolution at the Max Planck Institute for Developmental Biology, Tübingen, 2015. Web. 05 June 2015.
Foreach

**foreach** is a statement or construct featured in several higher programming languages.

C#
--

The foreach statement "repeats a group of embedded statements for each element in an array or an object collection that implements the System.CollectionsIEnumerable or System.Collections.GenericIEnumerableT interface. The foreach statement is used to iterate through the collection to get the information that you want, but can not be used to add or remove items from the source collection to avoid unpredictable side effects. If you need to add or remove items from the source collection, use a for loop".

## CMake

### 3.0.2

Foreach "evaluate[s] a group of commands for each value in a list".

## PHP

### PHP 4

The foreach "construct provides an easy way to iterate over arrays. foreach works only on arrays and objects, and will issue an error when you try to use it on a variable with a different data type or an uninitialized variable".

### PHP 5

The foreach "construct provides an easy way to iterate over arrays. foreach works only on arrays and objects, and will issue an error when you try to use it on a variable with a different data type or an uninitialized variable".

## Tcl

### Version 8.6.4

The foreach command "implements a loop where the loop variable(s) take on values from one or more lists. In the simplest case there is one loop variable, varname, and one list, list, that is a list of values to assign to varname. The body argument is a Tcl script. For each element of list (in order from first to last), foreach assigns the contents of the element to varname as if the lindex command had been used to extract the element, then calls the Tcl interpreter to execute body".

## References

1. ↑ "Foreach, in (C# Reference)." *Microsoft Developer Network*. Microsoft, n.d. Web. 15 June 2015.
2. ↑ "Foreach." *CMake 3.0.2 Documentation*. Kitware, Inc., n.d. Web. 15 June 2015.
3. ↑ 3.0 3.1 "Foreach - Manual." PHP. The PHP Group, n.d. Web. 15 June 2015.
4. ↑ "Foreach Manual Page - Built-In Commands." *Tcl8.6.4/Tk8.6.4 Documentation*. Sun Microsystems, Inc., n.d. Web. 15 June 2015.
Conceptual proteome

The **conceptual proteome** or **predicted proteome** (sometimes erroneously referred to as the proteome) is the "set of potential proteins inferred from a genome sequence".

## 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/
Glycobiology

**Glycobiology** is "the study of the structure, biosynthesis, biology, and evolution of saccharides (sugar chains or glycans) that are widely distributed in nature, and the proteins that recognize them".

## References

1. ↑ Varki A, Sharon N. Historical Background and Overview. 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 1. Available from: http://www.ncbi.nlm.nih.gov/books/NBK1931/
Decidable problem

A **decidable problem** (also referred to as a **totally decidable problem**, **algorithmically solvable**, or **recursively solvable**) is a "decision problem that can be solved by an algorithm that halts on all inputs in a finite number of steps. The associated language is called a decidable language".

## References

1. ↑ Algorithms and Theory of Computation Handbook, CRC Press LLC, 1999, "decidable problem", in *Dictionary of Algorithms and Data Structures* [online], Vreda Pieterse and Paul E. Black, eds. 17 December 2004. (accessed 13 December 2015) Available from: http://www.nist.gov/dads/HTML/decidableProblem.html
Euclidean algorithm

The **Euclidean algorithm** (also referred to as **Euclid's algorithm**) is an "algorithm for finding the greatest common divisor of two numbers *a* and *b*. The algorithm can also be defined for more general rings than just the integers ℤ".

## References

1. ↑ Weisstein, Eric W. "Euclidean Algorithm." From *MathWorld*--A Wolfram Web Resource. http://mathworld.wolfram.com/EuclideanAlgorithm.html
Bioinformatics

**Bioinformatics** is defined as "research, development, or application of computational tools and approaches for expanding the use of biological, medical, behavioral or health data, including those to acquire, store, organize, archive, analyze, or visualize such data". It is also the name of an Oxford journal which focuses on "new developments in genome bioinformatics and computational biology" and a Wikibooks textbook pertaining to bioinformatics.

## Further Reading

* "NIH WORKING DEFINITION OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY." Biomedical Information Science & Technology Initiative. National Institutes of Health, 17 July 2000. Web. 12 June 2015.
* Yu, Ungsik, Sung Hoon Lee, Young Joo Kim, and Sangsoo Kim. "Bioinformatics in the Post-genome Era." *Journal of Biochemistry and Molecular Biology* 37.1 (2004): 75-82. Print.

## External Links

* Definition of Bioinformatics - Institut Pasteur
* What is bioinformatics|BioPlanet

## References

1. ↑ Fassler, Jan, and Peter Cooper. "Bioinformatics." *BLAST Glossary*. U.S. National Library of Medicine, 14 July 2011. Web. 05 June 2015.
2. ↑ "Bioinformatics." *Oxford Journals*. Oxford University Press, n.d. Web. 08 June 2015.
3. ↑ "Bioinformatics." Wikibooks. *MediaWiki*, 9 Dec. 2013. Web. 10 June 2015.
Drug

A **drug** is a "substance used in the diagnosis, treatment, or prevention of a disease or as a component of a medication".

## References

1. ↑ "drug." *American Heritage Dictionary of the English Language, Fifth Edition*. 2011. Houghton Mifflin Harcourt Publishing Company 1 Oct. 2015 <http://www.thefreedictionary.com/drug>
Dielectric constant

The **dielectric constant** is a "property of an electrical insulating material (a dielectric) equal to the ratio of the capacitance of a capacitor filled with the given material to the capacitance of an identical capacitor in a vacuum without the dielectric material".

## References

1. ↑ "dielectric constant". *Encyclopædia Britannica*. *Encyclopædia Britannica Online*. Encyclopædia Britannica Inc., 2015. Web. 27 Sep. 2015 <http://www.britannica.com/science/dielectric-constant>.
Global alignment

A **global alignment** is an alignment in which sequences are aligned in their entirety.

## 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/
Data

Data (singular ***datum***) are "distinct pieces of information, usually formatted in a special way".

The term "data" sometimes refers to **digital data**, which itself refers to either "data represented by discrete values or conditions, as opposed to analog data" or the "discrete representations of quantized values of variables".

Furthermore, sometimes the term "data" refers to **computer data**, which is simply "information required by the computer to be able to operate" and is stored in binary format.

## See Also

* Big data
* Data type

## References

1. ↑ Beal, Vangie. "Data." *Webopedia*. QuinStreet Inc., 2015. Web. 23 June 2015.
2. ↑ "Definition: Digital Data." *FS-1037C*. Institute for Telecommunication Sciences, 23 Aug. 1996. Web. 23 June 2015.
3. ↑ "Computer Data." *Basic Computer Tutorial*. The Computer Technology Documentation Project, n.d. Web. 23 June 2015.
Drug eruption

## External Links

* Drug allergy - Mayo Clinic
* Drug Eruptions and Reactions - Dermatologic Disorders - Merck Manuals Professional Edition
* Drug-induced skin reactions (Anne Lee and John Thomson)

## Further Reading

* Nayak, Surajit, and Basanti Acharjya. “ADVERSE CUTANEOUS DRUG REACTION.” *Indian Journal of Dermatology* 53.1 (2008): 2–8. PMC. Web. 10 Sept. 2015.
ChIP-seq

**Chromatin-immunoprecipitation** (**ChIP**) **sequencing** (**ChIP-seq** or **ChIP/SEQ**) is a "technique involving size selection, high throughput sequencing (typically using next generation sequencing technologies that produce millions of reads in a run) and mapping of ChIP purified DNA onto a reference genome to achieve genome-wide identification of protein-DNA interactions".

## Further Reading

* Landt, Stephen G. et al. “ChIP-Seq Guidelines and Practices of the ENCODE and modENCODE Consortia.” *Genome Research* 22.9 (2012): 1813–1831. *PMC*. Web. 17 Oct. 2015.

## References

1. ↑ "Genome Glossary." *NCBI*. U.S. National Library of Medicine, n.d. Web. 17 Oct. 2015.
Constitutional unit

A **constitutional unit** is an "atom or group of atoms (with pendant atoms or groups, if any) comprising a part of the essential structure of a macromolecule, an oligomer molecule, a block, or a chain".

## References

1. ↑ Jenkins, A. D., P. Kratochvìl, R. F. T. Stepto, and U. W. Suter. "Glossary of Basic Terms in Polymer Science." *International Union of Pure and Applied Chemistry*. International Union of Pure and Applied Chemistry, 25 Oct. 1999. Web. 06 June 2015.
Connected graph

A **connected graph** is a "undirected graph that has a path between every pair of vertices".

## References

1. ↑ Paul E. Black, "connected graph", in *Dictionary of Algorithms and Data Structures* [online], Vreda Pieterse and Paul E. Black, eds. 19 April 2004. (accessed 21 Oct. 2015) Available from: http://www.nist.gov/dads/HTML/connectedGraph.html
Cut vertex

A **cut vertex** or **articulation point** is a "vertex whose deletion along with incident edges results in a graph with more components than the original graph".

## External Links

* Articulation Points Tutorial - YouTube
* Articulation Points - Harder Example - YouTube

## References

1. ↑ Algorithms and Theory of Computation Handbook, CRC Press LLC, 1999, "cut vertex", in *Dictionary of Algorithms and Data Structures* [online], Vreda Pieterse and Paul E. Black, eds. 17 December 2004. (accessed 21 Oct. 2015) Available from: http://www.nist.gov/dads/HTML/cutvertex.html
CDD

The **Conserved Domain Database** (**CDD**) is a "resource for the annotation of functional units in proteins. Its collection of domain models includes a set curated by NCBI, which utilizes 3D structure to provide insights into sequence/structure/function relationships".

## References

1. ↑ "Home - Conserved Domains - NCBI." *National Center for Biotechnology Information*. U.S. National Library of Medicine, n.d. Web. 20 July 2015.
EMBOSS Tools

**EMBOSS Tools**or **EMBOSS Programs** is an EMBL-EBI selection of "EMBOSS tools for sequence analysis, providing: pairwise sequence alignment, sequence format conversion, sequence translation and back-translation, and sequence statistics".

## Pairwise Sequence Alignment

* Needle
* Stretcher
* Water
* Matcher

## Sequence Translation

* Transeq
* Sixpack
* Backtranseq
* Backtranambig

## Sequence Statistics

* Pepinfo
* Pepstats
* Pepwindow
* Cpgplot
* Newcpgreport
* Isochore

## References

1. ↑ "Services A to Z, All Services." *EMBL-EBI*. EMBL-EBI, 2015. Web. 17 July 2015.
Glycolysis

**Glycolysis** (sometimes referred to as the **Embden-Meyerhof pathway**) is a "metabolic pathway whereby sugars are degraded anaerobically to lactate or pyruvate in the cytosol with the production of ATP".

## 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/
European Medicines Agency

The **European Medicines Agency** (**EMA**, previously known as the **European Agency for the Evaluation of Medicinal Products**) is a "decentralised agency of the European Union, located in London" which is "responsible for the scientific evaluation of medicines developed by pharmaceutical companies for use in the European Union".

## References

1. ↑ "About Us." *European Medicines Agency*. EMA, n.d. Web. 02 Oct. 2015.
Dense graph

A **dense graph** is a "graph in which the number of edges is close to the possible number of edges".

## References

1. ↑ Paul E. Black, "dense graph", in *Dictionary of Algorithms and Data Structures* [online], Vreda Pieterse and Paul E. Black, eds. 14 August 2008. (accessed 21 Oct. 2015) Available from: http://www.nist.gov/dads/HTML/densegraph.html
Extraction, transformation, and loading

**Extraction, transformation, and loading**, usually shortened to **ETL** but also referred to as **extract, transform, load**, refers to the "process of extracting data from source systems and bringing it into the data warehouse".

## References

1. ↑ "Overview of Extraction, Transformation, and Loading." *Database Data Warehousing Guide*. Oracle, 2015. Web. 03 Sept. 2015.
Cryptogene

A **cryptogene** is "one of several genes in the trypanosome mitochondrial genome which specify abbreviated RNAs that must undergo pan-editing in order to become functional".

## References

1. ↑ Brown TA. *Genomes*. 2nd edition. Oxford: Wiley-Liss; 2002. Glossary. Available from: http://www.ncbi.nlm.nih.gov/books/NBK21126/
Evolution

**Biological evolution** (more often simply referred to as **evolution**) is "descent with modification. This definition encompasses small-scale evolution (changes in gene frequency in a population from one generation to the next) and large-scale evolution (the descent of different species from a common ancestor over many generations). Evolution helps us to understand the history of life".

## References

1. ↑ "An Introduction to Evolution." *Understanding Evolution*. Niversity of California Museum of Paleontology, 22 Aug. 2008. Web. 22 June 2015.
Germline

The **germline** is the "cell line from which egg or sperm cells (gametes) are derived".

## 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/
Exon

An **exon** is a segment of a "eukaryotic gene (or of its primary transcript) that reaches the cytoplasm as part of a mature mRNA, rRNA, or tRNA molecule".

## 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/
Discovery phase

The **discovery phase** is the "first phase in the omics-based test development process during which candidate omics-based tests are first identified and confirmed on an independent set of specimens, if available".

## 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/
Graph pattern

A **graph pattern** is a "graph with wildcards, used to match against a data graph to specify desired results".

## External Links

* Graph Patterns - SPARQL Query Language for RDF

## References

1. ↑ Allemang, Dean, and James A. Hendler. *Semantic Web for the Working Ontologist: Effective Modeling in RDFS and OWL*. 2nd ed. Waltham: Morgan Kaufmann/Elsevier, 2011. Print.
Folding funnel

A **folding funnel** (also known as a **protein folding funnel**, **free energy funnel**, in some cases, **funnel concept** or **folding funnel hypothesis**) is the "hypothesized shape of the folding energy landscape. A funneled energy landscape will efficiently guide a folding protein to the native conformation, proposed to be the energetic minimum, without needing to sample all possible conformations".

## Further Reading

* Karplus, Martin. "Behind the Folding Funnel Diagram." *Nature Chemical Biology* 7.7 (2011): 401-04. Print.
* Onuchic, José Nelson, Nicholas D. Socci, Zaida Luthey-Schulten, and Peter G. Wolynes. "Protein Folding Funnels: The Nature of the Transition State Ensemble." *Folding and Design* 1.6 (1996): 441-50. Print.

## References

1. ↑ Bradshaw, Ralph A., and Philip D. Stahl, eds. *Encyclopedia of Cell Biology*. Amsterdam: Elsevier, Academic, 2015. Print.
HHalign

**HHalign** (sometimes stylized as **HHAlign**) is a tool which "compares two alignments with each other by pairwise alignment of HMMs".

## References

1. ↑ "Alignment Tools." *Bioinformatics Toolkit*. Department of Protein Evolution at the Max Planck Institute for Developmental Biology, Tübingen, 2015. Web. 05 June 2015.
EOL

The **Encyclopedia of Life** (**EOL**) is a website that "began in 2007 with the bold idea to provide a webpage for every species. EOL brings together trusted information from resources across the world such as museums, learned societies, expert scientists, and others into one massive database and a single, easy-to-use online portal at EOL.org".

## References

1. ↑ "EOL History." *Encyclopedia of Life*. N.p., n.d. Web. 05 June 2015.
Gap

A **gap** is a "space introduced into an alignment to compensate for an insertion or deletion in one aligned sequence relative to the other(s); typically designated by a dash".

## 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/
Conserved DNA sequence

A **conserved DNA sequence** is a cluster of "nucleotides that occur more often than would be predicted by random chance" and which "include a number of transcription start regions called promoters and many others".

## References

1. ↑ "conserved DNA sequences." *Saunders Comprehensive Veterinary Dictionary, 3 ed.*. 2007. Elsevier, Inc. 10 Oct. 2015 <http://medical-dictionary.thefreedictionary.com/conserved+DNA+sequences>
Chaperone

A **chaperone** (sometimes referred to as a **molecular chaperone** or **chaperone protein**) is a "protein required for the proper folding and/or assembly of another protein or protein complex".

## Further Reading

* Beissinger, M., and J. Buchner. "How Chaperones Fold Proteins." *Biological Chemistry* 379.3 (1998): 245-59. Print.
* Hendrick, J. P., and F. U. Hartl. "The Role of Molecular Chaperones in Protein Folding." *FASEB* Journal 9.15 (1995): 159-569. Print.
* Saibil, Helen. "Chaperone Machines for Protein Folding, Unfolding and Disaggregation." *Nature Reviews Molecular Cell Biology* 14.10 (2013): 630-42. Print.

## References

1. ↑ "Chaperone proteins." *Farlex Partner Medical Dictionary*. 2012. Farlex 11 Oct. 2015 <http://medical-dictionary.thefreedictionary.com/Chaperone+proteins>
Convolutional neural network

A **convolutional neural network** (variously abbreviated as **CNN** or **ConvNet**) is a hierarchical neural network whose convolutional layers alternate with subsampling layers, remiscent of simple and complex cells in the primary visual cortex.

## References

1. ↑ Ciresan, Dan C., Ueli Meier, Jonathan Masci, Luca M. Gambardella, and Jürgen Schmidhuber. "Flexible, High Performance Convolutional Neural Networks for Image Classification." *Proceedings of the Twenty-Second International Joint Conference on Artificial Intelligence* (2011): 1237-242. Print.
FRET sensor

**FRET sensors** are molecules or domains which "report changes in energy transfer between a donor and an acceptor fluorescent protein that occur when an attached sensor domain undergoes a change in conformation in response to ligand binding".

## References

1. ↑ Lindenburg, Laurens, and Maarten Merkx. “Engineering Genetically Encoded FRET Sensors.” *Sensors (Basel, Switzerland)* 14.7 (2014): 11691–11713. PMC. Web. 11 Oct. 2015.
Flow conservation

**Flow conservation** is the "property that no vertex, except the source and sink, of a flow network creates or stores flow. More formally, the incoming flow is the same as the outgoing flow, or, the net flow is 0".

## References

1. ↑ Algorithms and Theory of Computation Handbook, CRC Press LLC, 1999, "flow conservation", in *Dictionary of Algorithms and Data Structures* [online], Vreda Pieterse and Paul E. Black, eds. 17 December 2004. (accessed 15 November 2015) Available from: http://www.nist.gov/dads/HTML/flowconsrvtn.html
Growth factor

A **growth factor** is an "extracellular polypeptide molecule that binds to a cell-surface receptor triggering an intracellular signaling pathway leading to proliferation, differentiation, or other cellular response".

## 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/
Enzyme unit

An **enzyme unit** (**U**) is normally equal to the "amount of enzyme that catalyses the reaction of 1 µmol of substrate per minute".

However, a second definition defines an **enzyme unit** as the "amount of enzyme that catalyses the reaction of 1 nmol of substrate per minute".

## References

1. ↑ 1.0 1.1 *Enzyme Units, Activity and Specific Activity Explained*. Rep. N.p.: Innova Biosciences, n.d. Print.
Chimeric protein

A **chimeric protein** or **fusion protein** is a "hybrid protein encoded by a nucleotide sequence spliced together from 2+ complete or partial genes produced by recombinant DNA technology".

## References

1. ↑ "chimeric protein." *Segen's Medical Dictionary*. 2011. Farlex, Inc. 1 Nov. 2015 <http://medical-dictionary.thefreedictionary.com/chimeric+protein>
Dictionary

In computer science, a **dictionary** is an "abstract data type storing items, or values. A value is accessed by an associated key. Basic operations are new, insert, find and delete".

## References

1. ↑ Paul E. Black, "dictionary", 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/dictionary.html
Churchill

**Churchill** is a deterministic, highly scalable and balanced parallelization strategy "which fully automates the analytical process required to perform the complex and computationally intensive process of alignment, post-alignment processing, local realignment, recalibration and genotyping".

## Further Reading

* Kelly, Benjamin J., James R. Fitch, Yangqiu Hu, Donald J. Corsmeier, Huachun Zhong, Amy N. Wetzel, Russell D. Nordquist, David L. Newsom, and Peter White. "Churchill: An Ultra-fast, Deterministic, Highly Scalable and Balanced Parallelization Strategy for the Discovery of Human Genetic Variation in Clinical and Population-scale Genomics." *Genome Biology* 16.1 (2015): 6. Print.

## References

1. ↑ "Churchill." *The Research Institute at Nationwide Children's Hospital*. Nationwide Children's Hospital, 2015. Web. 03 Sept. 2015.
Gaussian white noise

**Gaussian white noise** (**GWN**) is a "stationary and ergodic random process with zero mean that is defined by the following fundamental property: *any two values of GWN are statistically independent no matter how close they are in time*.

## References

1. ↑ Marmarelis, Vasilis Z. *Nonlinear Dynamic Modeling of Physiological Systems*. Hoboken: Wiley-Interscience, 2004. Print.
Covalent bond

A **covalent bond** is a "region of relatively high electron density between nuclei which arises at least partly from sharing of electrons and gives rise to an attractive force and characteristic internuclear distance".

## See Also

* Agostic
* Coordination
* Hydrogen bond
* Multi-center bond

## 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.
Connectomics

**Connectomics** refers to the "comprehensive mapping and analysis of brain connectivity, across all scales, from the micro-scale of individual synaptic connections between neurons to the macro-scale of brain regions and interregional pathways".

## References

1. ↑ Behrens, Timothy EJ, and Olaf Sporns. "Human Connectomics." *Current Opinion in Neurobiology* 22 (2011): 1-10. Print.
Cycle

A **cycle** (also referred to as a **circuit** or **closed path**; or rarely as a **graph cycle**) is a "path that starts and ends at the same vertex and includes at least one edge".

## Further Reading

* Weisstein, Eric W. "Graph Cycle." From *MathWorld*--A Wolfram Web Resource. http://mathworld.wolfram.com/GraphCycle.html

## References

1. ↑ Paul E. Black, "cycle", in *Dictionary of Algorithms and Data Structures* [online], Vreda Pieterse and Paul E. Black, eds. 4 November 2009. (accessed 21 Oct. 2015) Available from: http://www.nist.gov/dads/HTML/cycle.html
Grep

**grep** (**global regular expression print**) is a command which "prints lines that contain a match for a pattern".

## References

1. ↑ "In Unix, What Do Some Obscurely Named Commands Stand For?" *Indiana University Knowledge Base*. The Trustees of Indiana University, 07 June 2012. Web. 28 Sept. 2015.
2. ↑ "GNU Grep 2.21." *GNU Operating System*. Free Software Foundation, Inc., 2014. Web. 28 Sept. 2015.
Germline mosaicism

**Germline mosaicism** (formerly known as **gonadal mosaicism**) refers to "two or more genetic or cytogenetic cell lines confined to the precursor (germline) cells of the egg or sperm".

## 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/
First-in, first-out

"**First-in, first-out**" (**FIFO**) is a "policy that items are processed in order of arrival. A queue implements this".

## References

1. ↑ Paul E. Black, "first-in, first-out", in *Dictionary of Algorithms and Data Structures* [online], Vreda Pieterse and Paul E. Black, eds. 17 December 2004. (accessed 21 Oct. 2015) Available from: http://www.nist.gov/dads/HTML/firstinfrstt.html
Glycome

The **glycome** is the "complete repertoire of glycans and glycoconjugates that cells produce under specified conditions of time, space, and environment".

## 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/
Greatest common divisor

The **greatest common divisor** (**GCD** or **gcd**) or **highest common divisor** is the largest divisor common to given positive integers *a* and *b*.

## References

1. ↑ Weisstein, Eric W. "Greatest Common Divisor." From *MathWorld*--A Wolfram Web Resource. http://mathworld.wolfram.com/GreatestCommonDivisor.html
Chimeric alignment

A **chimeric alignment** is an "alignment of a read that cannot be represented as a linear alignment. A chimeric alignment is represented as a set of linear alignments that do not have large overlaps. Typically, one of the linear alignments in a chimeric alignment is considered the “representative” alignment, and the others are called “supplementary” and are distinguished by the supplementary alignment flag. All the SAM records in a chimeric alignment have the same `QNAME` and the same values for 0x40 and 0x80 flags []. The decision regarding which linear alignment is representative is arbitrary".

## References

1. ↑ The SAM/BAM Format Specification Working Group. "Sequence Alignment/Map Format Specification." *GitHub*. GitHub, Inc., 28 Aug. 2015. Web. 14 Oct. 2015.
Electrospray ionization mass spectrometry

## External Links

* Electrospray Ionization Mass Spectrometry - ChemWiki

## Further Reading

* Banerjee, Shibdas, and Shyamalava Mazumdar. "Electrospray Ionization Mass Spectrometry: A Technique to Access the Information beyond the Molecular Weight of the Analyte." *International Journal of Analytical Chemistry* 2012 (2012): 1-40. Print.
Entropy

In information theory, mathematics and statistics, **entropy** (also referred to as **Shannon entropy** or **Shannon's entropy** after Claude E. Shannon or simply as **information entropy**, **statistical entropy** or **uncertainty**) refers to "a mathematical measure of the degree of randomness in a set of data, with greater randomness implying higher entropy and greater predictability implying lower entropy".

In physics, **entropy** refers to the "amount of 'disorder' of a system".

## External Links

* Information entropy | Modern Information Theory | Khan Academy

## References

1. ↑ "Shannon's entropy." *American Heritage Dictionary of the English Language, Fifth Edition*. 2011. Houghton Mifflin Harcourt Publishing Company 1 Oct. 2015 <http://www.thefreedictionary.com/Shannon%27s+entropy>
2. ↑ Weisstein, Eric W. "Entropy." From *MathWorld*--A Wolfram Web Resource. <http://mathworld.wolfram.com/Entropy.html>
Graph

A **graph** is a "set of items connected by edges. Each item is called a vertex or node. Formally, a graph is a set of vertices and a binary relation between vertices, adjacency".

## External Links

* Data structures: Introduction to graphs

## References

1. ↑ Paul E. Black and Paul J. Tanenbaum, "graph", in *Dictionary of Algorithms and Data Structures* [online], Vreda Pieterse and Paul E. Black, eds. 13 April 2015. (accessed 21 Oct. 2015) Available from: http://www.nist.gov/dads/HTML/graph.html
Growing fork

A **growing fork** (also referred to as a **replication fork**) is a "site in double-stranded DNA at which the template strands are separated and addition of deoxyribonucleotides to each newly formed chain occurs".

## 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/
Electric charge

**Electric charge** (or simply **charge**) is a "basic property of matter carried by some elementary particles. Electric charge, which can be positive or negative, occurs in discrete natural units and is neither created nor destroyed".

## References

1. ↑ "Electric charge". *Encyclopædia Britannica*. *Encyclopædia Britannica Online*. Encyclopædia Britannica Inc., 2015. Web. 8 Nov. 2016 <https://www.britannica.com/science/electric-charge>.
Computer science

**Computer science** is the "study of the storage, transformation and transfer of information. The field encompasses both the theoretical study of algorithms (including their design, efficiency and application) and the practical problems involved in implementing them in terms of computer software and hardware".

## References

1. ↑ "Computer Science Definition." The Linux Information Project (LINFO). The Linux Information Project, 31 Jan. 2006. Web. 06 June 2015.
Double hashing

**Double hashing** refers to a "method of open addressing for a hash table in which a collision is resolved by searching the table for an empty place at intervals given by a different hash function, thus minimizing clustering".

## References

1. ↑ Paul E. Black, "double hashing", in *Dictionary of Algorithms and Data Structures* [online], Vreda Pieterse and Paul E. Black, eds. 16 November 2009. (accessed 12 Oct. 2015) Available from: http://www.nist.gov/dads/HTML/doublehashng.html
FORTRAN

**FORTRAN** (sometimes written as **Fortran**; originally derived from **Formula Translating System**) is a "computer programming language that resembles algebra in its notation and is widely used for scientific applications".

## References

1. ↑ "FORTRAN." *Merriam-Webster*. Merriam-Webster, Incorporated, n.d. Web. 17 July 2015.
Disulfide

A **disulfide** or **disulphide** may refer to either a sulfide "containing two atoms of [sulfur] in its molecule or empirical formula" or an "organic compound containing the group —S—S— bonded to other groups".

## References

1. ↑ "Definition of Disulphide in English." *Oxford Dictionary*. Oxford University Press, 2015. Web. 08 Sept. 2015.
Dimensionality reduction

**Dimensionality reduction** or **dimension reduction** (sometimes referred to as **data dimensionality reduction**) is the "study of methods for reducing the number of dimensions describing an object".

## See Also

* Dimensionality
* Feature extraction
* Feature selection

## References

1. ↑ Dash, Manoranjan, and Huan Liu. "Dimensionality Reduction." (n.d.): n. pag. Web. 9 June 2016.
Dissociation constant

A **dissociation constant** (***Kd***) is the equilibrium constant for a reversible dissociation; it is a "constant that reflects the amount of energy that is required to separate two interacting molecules".

## References

1. ↑ "Glossary Terms : ChIP-seq and Beyond: New and Improved Methodologies to Detect and Characterize Protein-DNA Interactions : Nature Reviews Genetics." *Nature Reviews Genetics*. Macmillan Publishers Limited, n.d. Web. 17 Oct. 2015.
Data structure

In computer programming, a **data structure** is a "scheme for organizing related pieces of information. The basic types of data structures include:

* files
* lists
* arrays
* records
* trees
* tables

Each of these basic structures has many variations and allows different operations to be performed on the data".

## References

1. ↑ Beal, Vangie "Data Structure." *Webopedia*. QuinStreet Inc., 2015. Web. 11 November 2016.
Free software

**Free software** (also known as **libre software**) refers to "software that respects users' freedom and community. Roughly, it means that the users have the freedom to run, copy, distribute, study, change and improve the software".

## References

1. ↑ "What Is Free Software?" *GNU Project - Free Software Foundation*. Free Software Foundation, Inc., 17 Feb. 2015. Web. 06 June 2015.
Directed graph

A **directed graph** is a "graph whose edges are ordered pairs of vertices. That is, each edge can be followed from one vertex to another vertex".

## References

1. ↑ Paul E. Black, "directed graph", in *Dictionary of Algorithms and Data Structures* [online], Vreda Pieterse and Paul E. Black, eds. 20 November 2008. (accessed 21 Oct. 2015) Available from: http://www.nist.gov/dads/HTML/directedGraph.html
Genotype-phenotype correlation

The **genotype-phenotype correlation** refers to the "association between the presence of a certain mutation or mutations (genotype) and the resulting pattern of abnormalities (phenotype)".

## See Also

* Genotype
* Phenotype

## 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/
Codon bias

**Codon bias** refers to the "fact that not all codons are used equally frequently in the genes of a particular organism".

## Further Reading

* Clark, Nathan L., Eric Alani, and Charles F. Aquadro. “Evolutionary Rate Covariation in Meiotic Proteins Results from Fluctuating Evolutionary Pressure in Yeasts and Mammals.” *Genetics* 193.2 (2013): 529–538. PMC. Web. 28 June 2015.

## References

1. ↑ Brown TA. *Genomes*. 2nd edition. Oxford: Wiley-Liss; 2002. Glossary. Available from: http://www.ncbi.nlm.nih.gov/books/NBK21126/