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Programming Language  Instructions (syntax) to a computer to perform a calculation

(algorithm or program), such as sequence analysis. Popular programming languages are,

for example, Perl, Java, Python or C + +.

Promoter  gene readout start sequence.

Protein  see Proteins. 

Protein Domain  A self-contained folding unit in a protein, is about 100–150 amino acids

in size, has a specific molecular function, e.g. catalytic function, cofactor binding (e.g. for

cofactors such as NADH, FAD), interaction domain (between two domains in the protein

or a whole protein) and regulatory function (e.g. DNA binding or transmitting a signal). 

Proteins  Proteins. Most important building material of the cell (proteos, the first): all

enzymes (accelerate biochemical reactions in the cell) and important structural proteins

(collagen, e.g. hair; albumin in the blood, etc.). Proteins are made up of amino acids. The

20 most important (“proteinogenic amino acids”) are assembled with the help of the

genetic code according to the building instructions of the mRNA in the ribosome. Proteins

are therefore products of translation. Afterwards, proteins can be modified further (post-

translational modifications, e.g. sugar residues or lipid residues are retained). Proteins are

large molecules (macromolecules) with specific functions, for example as enzymes or

transcription factors. Their three-­dimensional structure and amino acid sequence are deci­

sive for the function. 

Protein Kinases  Enzymes that transfer phosphate residues (phosphotransferases) and

have an activating effect.

Protein Phosphatases  Enzymes that remove phosphate residues and have an inhibitory

effect. 

Protein Structure  Structure of a protein that is responsible for its function. A distinction

is made between primary structure (amino acid sequence), secondary structure (α-helix,

β-sheet), tertiary structure (single protein chain from several secondary structures) and

quaternary structure (several tertiary structures, i.e. several protein chains, often important

for cooperative structural adaptation).

Proteomics  Analysis of the proteome, the totality of all proteins.  PSSM (Position-

Specific Scoring Matrix; Often also Called Position-Specific Weight Matrix, PSWM)

Alternative to the consensus sequence, which specifically allows the prediction of these

motif patterns in other or new unknown sequences, such as transcription factor binding

sites (see also consensus sequence). 

p-Value  Statistical parameter indicating how likely it is to get the hit by chance. 

Quaternary Structure  see protein structure. 

18  Glossary