recursal/Fanatic-Fandom huggingface dataset:
EMBLog Bioinformatics Glossary

The **EMBLog Bioinformatics Glossary** is part of the EMBLog Glossary.

A

* Accession number
* Allele
* Alpha-helix (α-helix)
* Annotation
* Astex Viewer

B

* Balls and sticks representation (molecular structures)
* Beta-sheet (β-sheet)
* Bioinformatics
* BLAST

C

* Cheminformatics
* Chromophore
* ClustalW
* Computational biology
* Consensus gene sequence
* Contig
* Convergent evolution
* CRAM
* Curation

D

* Dimer
* Distributed Annotation System (DAS)
* Divergent evolution
* DNA

E

* EMBOSS Needle
* EMBOSS Seqret
* EMBOSS Transeq
* Ensembl
* European Nucleotide Archive (ENA)

F

* FASTA

G

* G protein-coupled receptors
* Gene
* Genome
* Genome-wide association studies (GWAS)

H

* Heterotetramer
* Homologue
* Homotetramer

J

* JalView
* Jmol

L

* Locus

M

* Macromolecule
* Membrane topology
* Multiple sequence alignment
* MUSCLE
* Mutation

N

* Next-generation sequencing
* Nucleotide
* Nucleotide BLAST

O

* Open reading frame (ORF)
* Opsin
* Orthologue
* Outgroup

P

* Pairwise alignment
* Paralogue
* Phylogenetic tree
* Phylogenetics
* Protein BLAST
* Protein Data Bank in Europe (PDBe)

R

* Reticulate evolution
* Ribbon diagram

S

* Sequencing Chromatogram

T

* Transmembrane domain
* Tripeptide

U

* UCSF Chimera
* Uniprot

X

* X-ray crystallography
Mappability

**Mappability** refers to the "uniqueness of a stretch of DNA sequence compared with a whole-genome sequence. Short sequence reads can be confidently mapped to unique sequence, but less confidently mapped to sequence that occurs multiple times in a genome".

## 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.
MSAProbs

**MSAProbs** is an "accurate multiple alignment algorithm for protein sequences. The design of MSAProbs is based on a combination of pair hidden Markov models and partition functions to calculate posterior probabilities".

## External Links

* MSAProbs - Parallel and accurate multiple sequence alignment

## References

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

**Metabolomics** is the "study of small-molecule metabolite profiles which specific cellular processes leave behind".

## References

1. ↑ "Institute of Bioinformatics and Systems Biology: Institute » Groups » Metabolomics » About Us." *Institute of Bioinformatics and Systems Biology*. Helmholtz Zentrum München Deutsches Forschungszentrum Für Gesundheit Und Umwelt, n.d. Web. 08 June 2015.
Flow

**Flow** is a "measure of the maximum weight along paths in a weighted, directed graph".

## References

1. ↑ Paul E. Black, "flow", 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/flow.html
Last-in, first-out

"**Last-in, first-out**" is a "policy that the most recently arrived item is processed first. A stack implements this".

## References

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

**Hydrogen bonding** is an "interaction involving a hydrogen atom located between a pair of other atoms having a high affinity for electrons; such a bond is weaker than an ionic bond or covalent bond but stronger than van der Waals forces".

## References

1. ↑ "hydrogen bonding". *Encyclopædia Britannica*. *Encyclopædia Britannica Online*. Encyclopædia Britannica Inc., 2015. Web. 02 Sep. 2015
<http://www.britannica.com/science/hydrogen-bonding>.
Indole

**Indole** or **benzopyrrole** is a "heterocyclic organic compound occurring in some flower oils, such as jasmine and orange blossom, in coal tar, and in fecal matter".

## References

1. ↑ "indole". *Encyclopædia Britannica*. *Encyclopædia Britannica Online*.
Encyclopædia Britannica Inc., 2015. Web. 03 Sep. 2015
<http://www.britannica.com/science/indole>.
INSDC

The **International Nucleotide Sequence Database Collaboration** (**INSDC**) is a "long-standing foundational initiative that operates between DDBJ, EMBL-EBI and NCBI".

## Further Reading

* Karsch-Mizrachi, Ilene, Yasukazu Nakamura, and Guy Cochrane. “The International Nucleotide Sequence Database Collaboration.” *Nucleic Acids Research* 40.Database issue (2012): D33–D37. PMC. Web. 23 Oct. 2015.

## References

1. ↑ "International Nucleotide Sequence Database Collaboration." *International Nucleotide Sequence Database Collaboration*. International Nucleotide Sequence Database Collaboration, n.d. Web. 23 Oct. 2015.
Koff

***K*off** or ***K*r** is the rate constant for binding of an enzyme to a binding site.

## References

1. ↑ Adachi, Kengo, Kazuhiro Oiwa, Masasuke Yoshida, Takayuki Nishizaka, and Kazuhiko Kinosita. "Controlled Rotation of the F1-ATPase Reveals Differential and Continuous Binding Changes for ATP Synthesis." *Nature Communications* 3 (2012): 1022. Print.
Longest common subsequence

The **longest common subsequence** (**LCS**; sometimes referred to as the **longest common subsequence problem** or the **heaviest common subsequence**) refers to the "problem of finding a maximum length (or maximum weight) subsequence of two or more strings".

## References

1. ↑ Algorithms and Theory of Computation Handbook, CRC Press LLC, 1999, "longest common subsequence", in *Dictionary of Algorithms and Data Structures* [online], Vreda Pieterse and Paul E. Black, eds. 2 September 2014. (accessed 12 December 2015) Available from: http://www.nist.gov/dads/HTML/longestCommonSubsequence.html
Monochromator

A **monochromator** is an "optical device that transmits a mechanically selectable narrow band of wavelengths of electromagnetic radiation chosen from a wider range of wavelengths available at the input".

## 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.
List of human genes, genetic disorders, and traits by MIM number

## 100000–299999: Autosomal loci or phenotypes (entries created before May 15, 1994)

* 100100: Abdominal muscles, absence of, with urinary tract abnormality and cryptorchidism
* 100200: Abducens palsy
* 100300: Adams-Oliver syndrome 1; AOS1
* 100500: *Moved to 200150*
* 100600: Acanthosis nigricans
* 100700: Achard syndrome
* 100800: Achondroplasia; ACH
* 100880: Aconitase 1, soluble; ACO1
* 100900: *Moved to 100880*
* 101000: Neurofibromatosis, Type 2; NF2
* 101200: Apert syndrome
* 101400: Saethre-Chotzen syndrome; SCS
* 101600: Pfeiffer syndrome
* 101800: Acrodysostosis 1 with or without Hormone Resistance; ACRDYS1
* 101900: Acrokeratosis verruciformis; AKV
* 102000: Acroleukopathy, Symmetric
* 102100: Acromegaloid changes, cutis verticis gyrata, and corneal leukoma
* 102200: Pituitary adenoma, growth hormone-secreting, 1; PAGH1
* 102300: Restless legs syndrome, Susceptibility to, 1; RLS1
* 102400: Acroosteolysis
* 102500: Hajdu-Cheney syndrome; HJCYS
* 102600: Adenine phosphoribosyltransferase; APRT
* 102700: Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-negative, due to adenosine deaminase deficiency
* 102800: Adenosine triphosphatase deficiency, Anemia due to
* 102900: Adenosine triphosphate, Elevated, of Erythrocytes
* 103000: Adenylate kinase 1; AK1
* 103100: Adie pupil

## 600000 and above: Autosomal loci or phenotypes (entries created after May 15, 1994)

* 600000: Spondylocamptodactyly
* 600100: *Moved to 601792*
* 600200: *Moved to 133440*
* 600300: Solute carrier family 1 (Glial high affinity glutamate transporter), Member 2; SLC1A2
* 600400: Prolyl endopeptidase; PREP
* 600500: *Moved to 600758*
* 600600: Ephrin receptor EphB1; EPHB1
* 600700: Lim domain-containing preferred translocation partner in lipoma; LPP
* 600800: NGFIA-binding protein; NAB1
* 600900: Sarcoglycan, Beta; SGCB
* 601000: *Moved to 109170*
False negative

A **false negative** refers to the "error of failing to observe a difference when in truth there is one".

## 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/
Ion channel

An **ion channel** is a "pathway through a protein molecule or complex in a cell membrane that modulates the electrical potential across the membrane by controlling the passage of small inorganic ions into and out of the cell".

## References

1. ↑ "ion channel." *American Heritage Dictionary of the English Language, Fifth Edition*. 2011. Houghton Mifflin Harcourt Publishing Company 17 Dec. 2015 <http://www.thefreedictionary.com/ion+channel>
Keyspace

In cryptography, **keyspace** or **key space** refers to the "total number of possible values of keys in a cryptographic algorithm or other security measure such as a password".

## References

1. ↑ "Keyspace." *Computer Desktop Encyclopedia*. 1981-2015. The Computer Language Company Inc. 10 Oct. 2015 <http://encyclopedia2.thefreedictionary.com/Keyspace>
Load factor

**Load factor** (**α**) is the "number of elements in a hash table divided by the number of slots".

## References

1. ↑ Paul E. Black, "load factor", in *Dictionary of Algorithms and Data Structures* [online], Vreda Pieterse and Paul E. Black, eds. 17 December 2004. (accessed 12 Oct. 2015) Available from: http://www.nist.gov/dads/HTML/loadfactor.html
Linux Bible

The ***Linux Bible*** is a book written by Christopher Negus which serves is the "ultimate hands-on Linux user guide".

## Ninth Edition

The ninth edition "covers the latest versions of Red Hat Enterprise Linux 7 (RHEL 7), Fedora 21, and Ubuntu 14.04 LTS, and includes new information on cloud computing and development with guidance on Openstack and Cloudforms".

## Eighth Edition

The eighth edition "provides a complete tutorial packed with major updates, revisions, and hands-on exercises so that you can confidently start using Linux today".

## References

1. ↑ 1.0 1.1 "Linux Bible Paperback – April 27, 2015." *Amazon.com*. Amazon.com, Inc, n.d. Web. 16 June 2015.
2. ↑ "Linux Bible Paperback – September 11, 2012." *Amazon.com*. Amazon.com, Inc, n.d. Web. 16 June 2015.
Molecule

A **molecule** is an "electrically neutral entity consisting of more than one atom (n > 1). Rigorously, a molecule, in which n > 1 must correspond to a depression on the potential energy surface that is deep enough to confine at least one vibrational state".

## 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).
Irregular macromolecule

An **irregular macromolecule** is a "macromolecule, the structure of which essentially comprises the repetition of more than one type of constitutional unit, or a macromolecule the structure of which comprises constitutional units not all connected identically with respect to directional sense".

## 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.
Microsatellite instability

**Microsatellite instability** (**MSI**) refers to a "change that occurs in the DNA of certain cells (such as tumor cells) in which the number of repeats of microsatellites (short, repeated sequences of DNA) is different than the number of repeats that was in the DNA when it was inherited. The cause of microsatellite instability may be a defect in the ability to repair mistakes made when DNA is copied in the cell".

## References

1. ↑ "Definition of Microsatellite Instability." *NCI Dictionary of Cancer Terms*. National Cancer Institute, n.d. Web. 5 Dec. 2015.
MyDomains

**MyDomains** is an image creation tool which allows the user to "define the shape, colour, size and name of one or several domains" as well as mark "specific residues and ranges".

## References

1. ↑ Hulo, N., A. Bairoch, V. Bulliard, L. Cerutti, B. A. Cuche, E. De Castro, C. Lachaize, P. S. Langendijk-Genevaux, and C. J. A. Sigrist. "The 20 Years of PROSITE." *Nucleic Acids Research* 36.Database (2007): n. pag. Print.
High-content analysis

**High-content analysis** (**HCA**) or **high-content screening** (**HCS**) describes "a set of analytical methods using automated microscopy, multi-parameter image processing, and visualization tools to extract quantitative data from cell populations". HCA is also sometimes referred to erroneously as cellomics.

## References

1. ↑ "High-Content Screening (HCS)." *Thermo Fisher Scientific*. Thermo Fisher Scientific Inc., n.d. Web. 9 June 2016.
Homolog

A **homolog** or **homologue** may refer to "one member of a chromosome pair", "a gene similar in structure and evolutionary origin to a gene in another species", or, in evolution, "characteristics that are similar in different species because they come from a common ancestor".

## References

1. ↑ Lefers, Mark. "Homolog Definition." *Hedgehog Signaling Glossary*. Holmgren Lab, 26 July 2004. Web. 05 Dec. 2015.
Metagenomics

Metagenomics is the "study of genomic DNA obtained from microorganisms that cannot be cultured in the laboratory".

## Further Reading

* Wooley, John C., Adam Godzik, and Iddo Friedberg. "A Primer on Metagenomics." *PLoS Computational Biology* 6.2 (2010): n. pag. Print.

## External Links

* Nature Reviews Microbiology - Focus on Metagenomics

## References

1. ↑ *Metagenomics: A Review of Publications Featuring Illumina® Technology*. 2nd ed. N.p.: Illumina, 2013. Print.
Knowledge discovery in databases

**Knowledge discovery in databases** (**KDD**) refers to the non-trivial process "of identifying valid, novel, potentially useful, and ultimately understandable patterns in data".

## References

1. ↑ Freitas, Alex A. "Are We Really Discovering "Interesting" Knowledge From Data?" (n.d.): n. pag. *University of Kent School of Computing*. University of Kent. Web. 9 June 2016.
Derivative chromosome

**Derivative chromosome** is a "term used to denote an abnormal chromosome consisting of segments from two or more chromosomes joined together as a result of a translocation, insertion, or other rearrangement".

## References

1. ↑ Pagon RA, Adam MP, Ardinger HH, et al., editors. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2016. *Illustrated Glossary*. Available from: https://www.ncbi.nlm.nih.gov/books/NBK5191/
Multiple alignment

A **multiple alignment** is an alignment which consists of three or more aligned 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/
Health outcome of interest

A **health outcomes of interest** (**HOIs**) are a "subset of all conditions that are of importance due to their historical associations with drug toxicities, their medical significance, and/or public health implications".

## References

1. ↑ "Health Outcomes of Interest." *Observational Medical Outcomes Partnership*. Observational Medical Outcomes Partnership, n.d. Web. 03 Sept. 2015.
Genomic medicine

**Genomic medicine** is a "medical discipline that involves using genomic information about an individual as part of their clinical care (e.g., for diagnostic or therapeutic decision-making) and the other implications of that clinical use".

## References

1. ↑ "NHGRI Definition of ‘Genomic Medicine’." *NHGRI*. NHGRI, Aug. 2012. Web. 7 June 2015.
Linear alignment

A **linear alignment** is an "alignment of a read to a single reference sequence that may include insertions, deletions, skips and clipping, but may not include direction changes (i.e. one portion of the alignment on forward strand and another portion of alignment on reverse strand). A linear alignment can be represented in a single SAM record".

## References

1. ↑ The SAM/BAM Format Specification Working Group. "Sequence Alignment/Map Format Specification." *GitHub*. GitHub, Inc., 28 Aug. 2015. Web. 14 Oct. 2015.
Just Be Real

Theo started diving into everything he needed to know about self-employment, starting a business, taxes, and so on. It led him to the journey of personal development. Later he started one of the top 100 personal development sites - Just Be Real in November 2012. To share his “life” and express all the opinions he kept bottled up for so many years. Since then, Theo has been expressing himself and has learned how to attract 1,000,000’s visitors online.

## References

1. ↑ How IFTTT Can Make Your Life Easier | Fupping
Internal sort

**Internal sort** refers to any "sort algorithm which uses exclusively main memory during the sort. This assumes high-speed random access to all memory".

## References

1. ↑ Algorithms and Theory of Computation Handbook, CRC Press LLC, 1999, "internal sort", 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/internalsort.html
Life Science Directory

The **Life Science Directory** (formerly known as **Amos' WWW links page**) is a page current hosted by ExPASy which lists websites related to the life sciences (unfortunately it is no longer updated).

## Protein related databases

* UniProt
* Around UniProtKB
	+ HAMAP
	+ SwissVar
	+ UniPathway
	+ ViralZone
	+ HPI
	+ PPAP
	+ Tox-Prot
* Swiss Human Plasma protein dataset
* NCBI protein resources
* InterPro
* PROSITE
* BLOCKS
* Gene3D
* Panther
* Pfam
* PIRSF
* PRINTS
* ProDom
* SBASE
* SMART
* SUPERFAMILY
* STRING
* TIGRFAMs
* BIND
* DIP
* MINT
* HPRD
* IntAct
* BioGRID
* PPI
* PMD

## Biological journals and publishers

### Bioinformatics journals and newsletters

* Bioinformatics
* Briefings in Bioinformatics
* ISB
* BioInformer
* embnet.news
* NCBI Newsletter
* PDB Quarterly Newsletter
* B6
* GenomeWeb BioInform
* BITS

## External Links

* ExPASy: SIB Bioinformatics Resource Portal - Life Science Directory
Nearest neighbor analysis

**Nearest neighbor analysis** is a "well established technique for non-parametric density estimation, pattern recognition, memory-based reasoning, and vector quantization".

## References

1. ↑ Yianilos, Peter N. "Data Structures and Algorithms for Nearest Neighbor Search in General Metric Spaces." *Proceedings of the Fourth Annual ACM-SIAM Symposium on Discrete Algorithms* (1993): 311-21. Print.
Human paleogenetics

## External Links

* Human Paleogenetics - Zoological Institute, University of Bern, Switzerland

## Further Reading

* Anagnostou, Paolo, Marco Capocasa, Nicola Milia, Emanuele Sanna, Cinzia Battaggia, Daniela Luzi, and Giovanni Destro Bisol. "When Data Sharing Gets Close to 100%: What Human Paleogenetics Can Teach the Open Science Movement." *PLoS ONE* 10.3 (2015): n. pag. Print.
* Brandt, Guido, Anna Szécsényi-Nagy, Christina Roth, Kurt Werner Alt, and Wolfgang Haak. "Human Paleogenetics of Europe – The Known Knowns and the Known Unknowns." *Journal of Human Evolution* 79 (2015): 73-92. Print.
* Pilipenko, A. S. "Human Paleogenetics." *Russian Journal of Genetics: Applied Research* 4.4 (2014): 281-91. Print.
N

**N** may refer to:

* Asparagine
* Haplogroup N
* Newton
* Nitrogen
* Normal force
* Normality
* The ATC code for the nervous system
* The set of natural numbers

**n** may refer to:

* Amount of substance
* Nano-
* Neutron
* Neutron emission
* Number of moles
* The coordination number of a substance
* The sample size (subsample)
* The size of a statistical sample
* The optical refractive index of a material

***N*** may refer to:

* The sample size (full sample)

***n*** may refer to:

* The number of training samples in a multilayer perceptron
* The size of a statistical sample
Minimum spanning tree

A **minimum spanning tree** (**MST**; also referred to as a **shortest spanning tree**, abbreviated as **SST**) is a "minimum-weight tree in a weighted graph which contains all of the graph's vertices".

## References

1. ↑ Joseph L. Ganley, "minimum spanning tree", in *Dictionary of Algorithms and Data Structures* [online], Vreda Pieterse and Paul E. Black, eds. 2 September 2014. (accessed 15 November 2015) Available from: http://www.nist.gov/dads/HTML/minimumSpanningTree.html
Ford-Fulkerson method

The **Ford-Fulkerson method** is a method which, "given a flow function and its corresponding residual graph (a maximum-flow problem), [can] select a path from the source to the sink along which the flow can be increased and increase the flow. [It is then] repeat[ed] until there are no such paths".

## References

1. ↑ Paul E. Black, "Ford-Fulkerson method", 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/fordFulkerson.html
Levinthal's paradox

## Further Reading

* Ben-Naim, Arieh. "Levinthal’s Question Revisited, and Answered." *Journal of Biomolecular Structure and Dynamics* 30.1 (2012): 113-24. Print.
* Zwanzig, R, A Szabo, and B Bagchi. “Levinthal’s Paradox.” *Proceedings of the National Academy of Sciences of the United States of America* 89.1 (1992): 20–22. Print.
Mutation rate

**Mutation rate** is the "number of mutation events per gene per unit of time (for example, per cell generation). The proportion of mutations per cell division in bacteria or single-celled organisms or the proportion of mutations per gamete in higher organisms".

## References

1. ↑ Lefers, Mark. "Mutation Rate Definition." *Hedgehog Signaling Glossary*. Department of Molecular Biosciences, Northwestern University, 26 July 2004. Web. 14 Sept. 2015.
Hypotonic

**Hypotonic** refers to an "external solution whose solute concentration is low enough to cause water to move into cells due to osmosis".

## 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/
Markov property

The **Markov property** or **Markovian property** refers to "'locality' in space or time, such as Markov random fields and Markov chain[s]".

## 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.
Monomeric unit

A **monomeric unit** or **monomer unit** is the "largest constitutional unit contributed by a single monomer molecule to the structure of a macromolecule or oligomer molecule".

## 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.
Coaxial helix

A **coaxial helix** is one of two separate helical regions stacked in order to form a pseudo-continuous (quasi-continuous) helix. Coaxial helices are highly stabilizing tertiary interactions and are seen in several large RNA structures, including tRNA, pseudoknots, the group I intron P4-P6 domain, and in the Hepatitis Delta Virus ribozyme.

## References

1. ↑ Kim, S. H., J. L. Sussman, F. L. Suddath, G. J. Quigley, A. Mcpherson, A. H. J. Wang, N. C. Seeman, and A. Rich. "The General Structure of Transfer RNA Molecules." *Proceedings of the National Academy of Sciences* 71.12 (1974): 4970-974. Print.
Micelle

In physical chemistry, a **micelle** refers to a "loosely bound aggregation of several tens or hundreds of atoms, ions (electrically charged atoms), or molecules, forming a colloidal particle—i.e., one of a number of ultramicroscopic particles dispersed through some continuous medium".

## References

1. ↑ "micelle". *Encyclopædia Britannica*. *Encyclopædia Britannica Online*. Encyclopædia Britannica Inc., 2015. Web. 09 Sep. 2015
<http://www.britannica.com/science/micelle>.
Isozyme

An **isozyme** (often referred to as an **isoenzyme**) is "one of a group of related enzymes catalysing the same reaction but having different molecular structures and characterized by varying physical, biochemical and immunological properties".

## 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.
List of Galaxy tools

This is a list of all of the tools that are, or have been, available on the Galaxy Project server.

## Get Data

* Upload File from your computer
* UCSC Main table browser
* UCSC Archaea table browser
* EBI SRA ENA SRA
* BioMart Central server
* GrameneMart Central server
* Flymine server
* modENCODE fly server
* modENCODE modMine server
* MouseMine server
* Ratmine server
* YeastMine server
* modENCODE worm server
* WormBase server
* ZebrafishMine server
* EuPathDB server
* GenomeSpace import from file browser

## NGS: QC and manipulation

* FastQC Read Quality reports
* Select high quality segments
* Build base quality distribution
* Draw quality score boxplot
* Quality format converter (ASCII-Numeric)
* Filter by quality
* FASTQ to FASTA converter
* Remove sequencing artifacts
* Barcode Splitter
* Clip adapter sequences
* Collapse sequences
* Draw nucleotides distribution chart
* Compute quality statistics
* Rename sequences
* Reverse-Complement
* Trim sequences
* Combine FASTA and QUAL into FASTQ
* Filter FASTQ reads by quality score and length
* Manipulate FASTQ reads on various attributes
* FASTQ Groomer convert between various FASTQ quality formats
* FASTQ Masker by quality score
* FASTQ joiner on paired end reads
* FASTQ splitter on joined paired end reads
* FASTQ Summary Statistics by column
* FASTQ to FASTA converter
* FASTQ to Tabular converter
* FASTQ Trimmer by column
* FASTQ Quality Trimmer by sliding window
* Tabular to FASTQ converter
* Convert SOLiD output to fastq
* Compute quality statistics for SOLiD data
* Draw quality score boxplot for SOLiD data

## NGS: SAMtools

* bcftools view Converts BCF format to VCF format
* Reheader copy SAM/BAM header between datasets
* Split BAM dataset on readgroups
* Stats generate statistics for BAM dataset
* BAM-to-SAM convert BAM to SAM
* Sort BAM dataset
* CalMD recalculate MD/NM tags
* BedCov calculate read depth for a set of genomic intervals
* IdxStats tabulate mapping statistics for BAM dataset
* Flagstat tabulate descriptive stats for BAM datset
* Slice BAM by genomic regions
* SAM-to-BAM convert SAM to BAM
* RmDup remove PCR duplicates
* MPileup call variants
* Pileup-to-Interval condenses pileup format into ranges of bases
* Filter pileup on coverage and SNPs
* Convert SAM to interval
* Filter SAM on bitwise flag values
* Generate pileup from BAM dataset
* Filter SAM or BAM, output SAM or BAM files on FLAG MAPQ RG LN or by region
Linear probing

**Linear probing** refers to a "hash table in which a collision is resolved by putting the item in the next empty place in the array following the occupied place. Even with a moderate load factor, primary clustering tends to slow retrieval".

## References

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

**This page is under construction.**

*The creator of the article or topic may have more information to add in order to complete this page. If you have information you think is useful for this page, you can help by editing this page.*

 Species
 Gender
 Birth Date
 Occupation
owned by

**Toothbrush**, who currently has no confirmed name other than his alias, is a male contestant in Primi's Airplane Panic.

## Appearance

Toothbrush is a blue household toothbrush made of plastic. He has skinny black arms and legs, and beady black eyes. The brush above his face is colored bright yellow.

## Abilities and Combat Strategy

Toothbrush is unknown to have any combat experience whatsoever. The best he can do self-defense wise is squirt the enemy with toothpaste, or rub his brush against them (which does not normally damage anything). He may also resort to fist-fighting the enemy,

## Facts and Trivia

* Originally, Toothbrush was going to make his first appearance in a show by YearsAnimations called Object Redundancy. For an unknown reason, this idea was never used.

## Quotes

This character does not have any notable quotes.
Memoization

**Memoization** refers to the ability to "save (memoize) a computed answer for possible later reuse, rather than recomputing the answer".

## References

1. ↑ Paul E. Black, "memoization", in *Dictionary of Algorithms and Data Structures* [online], Vreda Pieterse and Paul E. Black, eds. 14 August 2008. (accessed 12 December 2015) Available from: http://www.nist.gov/dads/HTML/memoize.html
Mohammed Araan

Template:Infobox person

Mohammed Araan (Urdu:[ارائیں شیخ]; born December, 2004) is an inventor, researcher, developer, and CEO and Founder of TUMULL INC at a young age of 15 years. He has even made Discord Applications. Developed a App named PICK UP PODCAST. Started programming at a age of 14 years.
Araan is a self-taught programmer who started programming and coding at a very early age. Despite being so young, he learned the BASIC programming language. At age of 14 he made a App named PICK UP PODCAST.

## Developer

Mohammed Araan is a developer who is known for his work in Discord Applications.

Araan uses programming language to create Android Apps.

Araan is the chief executive officer and founder of TUMULL INC, an Indie company that makes Discord applications.

## Recognition

* Certified by IIT Bombay, Hardvard University, Stanford University
* Verified Android Apps Developer.
* Got Invitation to Samsung Developer live Conference.
* Developer of Apps at Indus OS

## Influence

Mohammed Araan has 10k+ followers on Instagram. He post things related to coding and spoiler of his upcoming projects.

## Personal Profile

Mohammed Araan was born in Udupi.
He had his Secondary Education in G M VIDYANIKETAN PUBLIC SCHOOL.

## Works

* Made an Android App named PICK UP PODCAST. A Podcast App where you can listen to Millions of Podcasts.
* CLOMEL UTILITY a Discord Application where people can use it in their servers. It has grabbed a badge as Popular Bot by bot.gg(A botlist site by Autocode).
* Co Founder of MUKHDHA DEVELOPMENT
Loss of heterozygosity

A **loss of heterozygosity** (**LOH**) refers to a "a deletion or other mutational event within the normal allele renders the cell either hemizygous (one deleterious allele and one deleted allele) or homozygous for the deleterious allele" at a particular locus heterozygous for a deleterious mutant allele and a normal allele.

## External Links

* Definition of loss of heterozygosity - NCI Dictionary of Genetics Terms - National Cancer Institute

## References

1. ↑ "Loss of Heterozygosity - Glossary Entry." *Genetics Home Reference*. National Institutes of Health (NIH), 30 Nov. 2015. Web. 05 Dec. 2015.
Inflection point

An **inflection point** is a "point on a curve at which the sign of the curvature (i.e., the concavity) changes. Inflection points may be stationary points, but are not local maxima or local minima. For example, for the curve *y* = *x*3 plotted above, the point *x* = 0 is an inflection point".

## References

1. ↑ Weisstein, Eric W. "Inflection Point." From *MathWorld*--A Wolfram Web Resource. http://mathworld.wolfram.com/InflectionPoint.html
Kruskal's algorithm

**Kruskal's algorithm** is an "algorithm for computing a minimum spanning tree. It maintains a set of partial minimum spanning trees, and repeatedly adds the shortest edge in the graph whose vertices are in different partial minimum spanning trees".

## External Links

* Kruskal's algorithm in 2 minutes - Review and example - YouTube
* KruskalMST.java

## References

1. ↑ Joseph L. Ganley, "Kruskal's algorithm", in *Dictionary of Algorithms and Data Structures* [online], Vreda Pieterse and Paul E. Black, eds. 19 April 2006. (accessed 15 November 2015) Available from: http://www.nist.gov/dads/HTML/kruskalsalgo.html
MUSCLE

**MUSCLE** (**Multiple Sequence Comparison by Log-Expectation**) is a "program for creating multiple alignments of protein sequences".

## External Links

* MUSCLE < Multiple Sequence Alignment < EMBL-EBI

## References

1. ↑ Edgar, Robert C. "MUSCLE: Multiple Sequence Alignment with High Accuracy and High Throughput." *Nucleic Acids Research* 32.5 (2004): 1792–1797. PMC. Web. 5 June 2015.
NP

In computational complexity theory, **NP** refers to the "complexity class of decision problems for which answers can be checked by an algorithm whose run time is polynomial in the size of the input. Note that this doesn't require or imply that an answer can be found quickly, only that any claimed solution can be verified quickly. "NP" is the class that a Nondeterministic Turing machine accepts in Polynomial time".

## References

1. ↑ Paul E. Black, "NP", in *Dictionary of Algorithms and Data Structures* [online], Vreda Pieterse and Paul E. Black, eds. 9 September 2013. (accessed 13 December 2015) Available from: http://www.nist.gov/dads/HTML/np.html
Linux Pocket Guide

The ***Linux Pocket Guide*** is a Linux textbook written by Daniel J. Barrett which provides "an organized learning path for Linux use, rather than Linux programming and system administration".

## References

1. ↑ "Linux Pocket Guide, 2nd Edition Paperback – March 30, 2012" *Amazon.com*. Amazon.com, Inc, n.d. Web. 16 June 2015.
Ion-exchange chromatography

**Ion-exchange chromatography** or **ion chromatography** is a "special form of adsorption chromatography where the adsorbent or stationary phase is an ion-exchange material and the mobile phase is an ionizing solvent".

## Further Reading

* *Ion Exchange Chromatography Principles*. N.p.: Amersham Pharmacia Biotech, 1999. Print.

## External Links

* Ion Chromatography
* Ion Exchange Chromatography - MIT OpenCourseWare

## References

1. ↑ Paech, Karl, and Hans F. Linskens. *Moderne Methoden Der Pflanzenanalyse*. Berlin: Springer-Verlag, 1962. Print.
NCBI

The **National Center for Biotechnology Information** (**NCBI**) is an "American resource for molecular biology information. Its mission is to develop new information technologies to aid in the understanding of fundamental molecular and genetic processes that control health and disease. More specifically, the NCBI has been charged with creating automated systems for storing and analyzing knowledge about molecular biology, biochemistry, and genetics; facilitating the use of such databases and software by the research and medical community; coordinating efforts to gather biotechnology information both nationally and internationally; and performing research into advanced methods of computer-based information processing for analyzing the structure and function of biologically important molecules".

## References

1. ↑ "General Introduction." *NCBI*. U.S. National Library of Medicine, 21 May 2004. Web. 05 June 2015.
In-place sort

An **in-place sort** is a "sort algorithm in which the sorted items occupy the same storage as the original ones. These algorithms may use *o*(*n*) additional memory for bookkeeping, but at most a constant number of items are kept in auxiliary memory at any time".

## References

1. ↑ Paul E. Black and Conrado Martinez, "in-place sort", in *Dictionary of Algorithms and Data Structures* [online], Vreda Pieterse and Paul E. Black, eds. 15 March 2004. (accessed 16 Oct. 2015) Available from: http://www.nist.gov/dads/HTML/inplacesort.html
MALDI-TOF

**MALDI-TOF** (**Matrix Assisted Laser Desorption Ionization Time-of-Flight**) is a "high-throughput protein sequencing method based on embedding samples in a matrix from which they are desorbed by laser light".

## References

1. ↑ "MALDI-TOF MS." *Segen's Medical Dictionary*. 2011. Farlex, Inc. 12 Oct. 2015 <http://medical-dictionary.thefreedictionary.com/MALDI-TOF+MS>
NP-hard

The phrase "**NP-hard**" refers to the "complexity class of decision problems that are intrinsically harder than those that can be solved by a nondeterministic Turing machine in polynomial time. When a decision version of a combinatorial optimization problem is proved to belong to the class of NP-complete problems, then the optimization version is NP-hard".

## References

1. ↑ Algorithms and Theory of Computation Handbook, CRC Press LLC, 1999, "NP-hard", in *Dictionary of Algorithms and Data Structures* [online], Vreda Pieterse and Paul E. Black, eds. 9 September 2013. (accessed 13 December 2015) Available from: http://www.nist.gov/dads/HTML/nphard.html
Informatics

**Informatics** is the "study of the structure, behaviour, and interactions
of natural and engineered computational systems" or, somewhat more broadly, the "study and application of information technology to the arts, science and professions, and to its use in organizations and society at large".

## References

1. ↑ "WHAT IS INFORMATICS?" *The University of Edinburgh*. The University of Edinburgh, 2015. Web. 7 June 2015.
2. ↑ "Informatics Defined." *IU School of Informatics and Computing*. The Trustees of Indiana University, n.d. Web. 06 June 2015.
Monomer

A **monomer** is a "substance composed of monomer molecules".

## 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.
Homology

**Homology** is "similarity of the structure, physiology, or development of different species of organisms based upon their descent from a common evolutionary ancestor".

## References

1. ↑ The Editors of Encyclopædia Britannica. "Homology (Evolution)." *Encyclopedia Britannica Online*. Encyclopedia Britannica, 2015. Web. 05 June 2015.
Molar extinction coefficient

The **molar extinction coefficient** (also known as the **molar attenuation coefficient** or **molar absorptivity**) is a "measure of the probability of the electronic transition".

## Further Reading

* Pace, C. N. et al. “How to Measure and Predict the Molar Absorption Coefficient of a Protein.” *Protein Science : A Publication of the Protein Society* 4.11 (1995): 2411–2423. Print.

## References

1. ↑ "Beer-Lambert Law." *OChemPal*. Utah Valley University, 2009. Web. 03 Sept. 2015.
Homeosis

**Homeosis** is the "transformation of one body part into another arising from mutation in or misexpression of certain developmentally critical genes".

## 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/
LZW algorithm

The **Lempel-Ziv-Welch** (**LZW**) **algorithm** (also known as **LZW compression**, **LZW data compression**, or simply **LZW**) is a "popular data compression technique developed in 1977 by J. Ziv and A Lempel, and later refined by Terry Welch. It is the compression algorithm used in the GIF graphics file format, which is one of the standard graphic formats used by CompuServe and the World Wide Web".

## External Links

* Interactive LZW Compression
* Lempel-Ziv-Welch
* Lempel-Ziv-Welch (LZW) Algorithm
* Lempel-Ziv-Welch Compression Algorithm - Tutorial - YouTube
* LZW coding 1 - YouTube
* LZW compression - Rosetta Code
* LZW Data Compression
* LZW Data Compression
* LZW.java

## References

1. ↑ "LZW." *Webopedia*. QuinStreet Inc., 2015. Web. 11 Oct. 2015.
K-D tree

A **K-D tree** (abbreviated from ***k*-dimensional tree**; also stylized as **KD tree**, ***k*-d tree**, **Kd-tree**, or **kd-tree**) is a generalization of a binary search tree that stores points in *k*-dimensional space.

## References

1. ↑ Precup, Mike. "Assignment 3: KDTree." *CS106L: Standard C++ Programming Laboratory*. Stanford University, 30 May 2016. Web. 10 June 2016.
K-Nearest neighbors algorithm

The ***k*-nearest neighbors algorithm** (variously abbreviated as ***k*-NN**, ***k*NN**, or **KNN**; also stylized as ***k*-th nearest neighbor algorithm** or ***k* nearest neighbor algorithm**; rarely also referred simply as the **nearest neighbors algorithm** or **nearest neighbors**) is an algorithm.

## See Also

* *k*-Nearest neighbor classification
* kNN classifier

## External Links

* The K-Nearest Neighbor Algorithm | Coursera
Lineweaver-Burk plot

A **Lineweaver-Burk plot** (sometimes referred to as a **Lineweaver Burke plot**) or **double-reciprocal plot** is a plot of 1/*V*0 versus 1/[S] which yields a straight line with an intercept of 1/*V*max and a slope of *K*M/*V*max. The intercept on the *x*-axis is -1/*K*M.

## External Links

* Enzymatic inhibition and Lineweaver Burke plots | Enzyme Kinetics | Khan Academy
* Enzyme Inhibition - ChemWiki

## References

1. ↑ Berg JM, Tymoczko JL, Stryer L. *Biochemistry*. 5th edition. New York: W H Freeman; 2002. Appendix: Vmax and KM Can Be Determined by Double-Reciprocal Plots. Available from: http://www.ncbi.nlm.nih.gov/books/NBK22557/
Hash function

A **hash function** is an "algorithm that turns a variable amount of text into a small, fixed-length value called a 'hash value' or "hash code'".

## References

1. ↑ "Hash (computer science)." *Computer Desktop Encyclopedia. 1981-2015*. The Computer Language Company Inc. 11 Oct. 2015 <http://encyclopedia2.thefreedictionary.com/Hash+(computer+science)>
Halting problem

The **halting problem** is the "problem of determining in advance whether a particular program or algorithm will terminate or run forever. The halting problem is the canonical example of a provably unsolvable problem. Obviously any attempt to answer the question by actually executing the algorithm or simulating each step of its execution will only give an answer if the algorithm under consideration does terminate, otherwise the algorithm attempting to answer the question will itself run forever".

## External Links

* The Craig Web Experience: Understanding the Halting Problem

## References

1. ↑ "halting-problem". *The Free On-line Dictionary of Computing*. Denis Howe. 13 Dec. 2015. <Dictionary.com http://dictionary.reference.com/browse/halting-problem>.
Isoelectric point

The **isoelectric point** (abbreviated **pI** or **IEP**; also variously referred to as the **isoelectronic point**, the **isoionic point**, or the **isoelectric pH**) is the "point or narrow range on a pH scale at which an amphoteric molecule or surface carries no electrical charge, or in which the negative and positive charges are equal resulting in a net zero charge".

## References

1. ↑ "Isoelectric Point." *Merriam-Webster*. Merriam-Webster, Incorporated, 2015. Web. 27 Sept. 2015.
Native protein

**Native protein** refers to the "concept of a protein in its natural state, in the cell, unaltered by heat, chemicals, enzyme action, or the exigencies of extraction".

## References

1. ↑ "native protein." *Farlex Partner Medical Dictionary*. 2012. Farlex 28 Sep. 2015 <http://medical-dictionary.thefreedictionary.com/native+protein>
Lactate dehydrogenase

**Lactate dehydrogenase** (**LD**, **LDH**) is an "enzyme that catalyzes the interconversion of lactate and pyruvate. It is widespread in tissues and is particularly abundant in kidney, skeletal muscle, liver, and myocardium".

## References

1. ↑ "LDH." *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/LDH>
Human microbiome

The **human microbiome** is the "full array of microorganisms (the microbiota) that live on and in humans and, more specifically, the collection of microbial genomes that contribute to the broader genetic portrait, or metagenome, of a human".

## References

1. ↑ "human microbiome". *Encyclopædia Britannica*. *Encyclopædia Britannica Online*.
Encyclopædia Britannica Inc., 2015. Web. 02 Sep. 2015
<http://www.britannica.com/science/human-microbiome>.
Interactive visualization

**Interactive visualization** is a quality of certain technologies which "enables the exploration of data via the manipulation of chart images, with the color, brightness, size, shape and motion of visual objects representing aspects of the dataset being analyzed".

## References

1. ↑ "Interactive Visualization - Gartner IT Glossary." *Gartner, Inc*. Gartner, Inc., 31 July 2012. Web. 07 June 2015.
List of degree granting programs in biomedical informatics by degree type

This is a **list of degree granting programs in biomedical informatics by degree type**. It therefore will not include degrees in bioinformatics, health informatics and other similar programs. Only degrees including "biomedical informatics" in the name should be included here.

## Graduate Programs

### Doctorate Degrees

#### Doctor of Philosophy (Ph.D.)

* Stanford University
* University of Cincinnati
HTML/JS: Making webpages interactive

***HTML/JS: Making webpages interactive*** is a Khan Academy course which teaches users how to "combine [their] knowledge of HTML/CSS with [their] knowledge of JavaScript to make your webpages interactive".

## References

1. ↑ "HTML/JS: Making webpages interactive." Khan Academy. Khan Academy, 2015. Web. 07 June 2015.
K-Nearest neighbor classification

***k*-Nearest neighbor classification** (**kNN classification**; also referred to as ***k*-nearest neighbor**, **memory-based reasoning**, **example-based reasoning**, **instance-based learning**, **case-based reasoning**, or **lazy learning**) is "one of the most fundamental and simple classification methods and should be one of the first choices for a classification study when there is little or no prior knowledge about the distribution of the data".

## References

1. ↑ Peterson, Leif E. "K-nearest Neighbor." *Scholarpedia*. MediaWiki, 21 Feb. 2009. Web. 9 June 2016.
Isoschizomer

An **isoschizomer** is a restriction endonuclease that contains an identical recognition site to another isoschizomer but is derived from a different species of bacteria (and hence has a different name)".

## References

1. ↑ Kaushansky, K. "Glossary of Molecular Biology Terminology." *Hematology* 2002.1 (2000): 490-509. Print.