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Moodle

A large dictionary of terminology used in bioinformatics, including relevant biology, chemistry, math and computer science terms.


Browse the glossary using this index

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A

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A is the single-letter amino acid code for Alanine.
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See PAM
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The three-letter amino acid code for Alanine.
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Alanine (A, ALA) is an aliphatic or "oily" amino acid that has a hydrophobic side chain.
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The juxtaposition of residues between two or more sequences along with gaps that models the evolutionary or functional changes between the sequences . Alignments can be global (showing the changes across the entire lengths of the sequences) or local (showing only the changes within the most conserved area of the sequences).
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A carbon molecule in an amino acid that is

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Regular secondary structure found in proteins where the backbone confirmation of each element assumes the same configuration. This confirmation yields a shape that is spiral.

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Part of an amino acid where the chemical structure containing nitrogen and hydrogen. (NH2)

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Amino acids are the building block of proteins. There are twenty common amino acids that are used in living organisms, plus a few atypical amino acids that are only utilized by a few organisms. See Central Dogma.
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ARG is the three-letter amino acid code for Arginine.
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Arginine (R, ARG) is a nitrogen containing (amine) amino acid that has a positively charged side chain.
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ASN is the three-letter amino acid code for Asparagine.
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ASP is the three-letter amino acid code for Aspartic Acid.
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Asparagine (N, ASN) is an amide containing amino acid that is uncharged and has polar side chains derived from acidic amino acids.

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Aspartic Acid (D, ASP) is an acidic amino acid that is negatively charged.
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ASX is the three-letter ambiguous amino acid code used to represent that the amino acid is either Aspartic Acid or Asparagine.

B

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B is the single-letter ambiguous amino acid code used to represent that the amino acid is either Aspartic Acid or Asparagine.
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A regular secondary structure found in proteins where the backbone confirmation of each element assumes the same configuration. This confirmation yields a shape that is (relatively) flat.

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  1. Basic Local Alignment Search Tool.
  2. Technique for aligning sequences that is typically used for database searching. BLAST is a heuristic to the more computationally demanding Dynamic Programming Algorithm. The original BLAST technique found long statistically-significant stretches without gaps. Subsequent improvements to the algorithm have added the capability to produce gapped alignments.
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A series of matrices created by Hennikoff and Hennikoff. This series is dependent on an implicit model of evolution derived from good scoring blocks of sequences. The matrix construction method uses sequence weighting using percent identity to correct for over-representation. The BLOSUM62 matrix in particular is very good at identifying sequences in a database search using the BLAST algorithm. The number associated with the Blosum matrix is associated with the percentage identity of the sequences in the blocks; thus the numbers are in the opposite direction that one would find when using the PAM model.
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In a phylogenetic tree a branch refers to the lines in the tree. These are sometimes called edges.

C

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C is the single-letter amino acid code for Cystine.
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The part of an amino acid containing Carbon double bonded to Oxygen.
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Part of an amino acid where the chemical structure contains carbon oxygen and hydrogen (COOH)

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The central dogma of molecular biology is about the flow of genetic information between DNA, RNA and protein molecules. In general this information flows from DNA to RNA then to Protein. While occasionally information can flow back from RNA to DNA, genetic information does not flows back from Protein to RNA or Protein to DNA.


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