Begriffe der Bioinformatik

 

BLAST

Basic local alignment search tool (Altschul et al., 1990)

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E value

E is the expected frequency of chance occurrence of a
high scoring pair HSP having score S (or one scoring higher).

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homologues

Divergent descendents of a common phylogenetic precursor.

 

HSP

The High-scoring Segment Pair (HSP) is the fundamental unit
of BLAST algorithm output. An HSP consists of two sequence
fragments of arbitrary but equal length whose alignment is
locally maximal and for which the alignment score meets or
exceeds a threshold or cutoff score.

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orthologues

Inter-species homologues generated by speciation.

 

PAM

point accepted mutation

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paralogues

Intra-species homologues generated by gene duplication.

 

P-Value

The Poisson P-value for any given HSP is a function of its
expected frequency of occurrence and the number of HSPs
observed against the same database sequence with scores at
least as high.

Details

Score

The raw score S for an alignment is calculated by summing the scores for each aligned position and the scores for gaps. In amino acid alignments, the score for an identity or a substitution is given by the specified substitution matrix. NIH Glossary

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Substitution Matrix

A substitution matrix containing values proportional to the probability that amino acid i mutates into amino acid j for all pairs of amino acids. NIH Glossary

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