FASTA (SOAP)

By | September 22, 2011

FASTA (pronounced FAST-AYE) stands for FAST-All, reflecting the fact that it can be used for a fast protein comparison or a fast nucleotide comparison. This program achieves a high level of sensitivity for similarity searching at high speed. This is achieved by performing optimised searches for local alignments using a substitution matrix. The high speed of this program is achieved by using the observed pattern of word hits to identify potential matches before attempting the more time consuming optimised search. The trade-off between speed and sensitivity is controlled by the ktup parameter, which specifies the size of the word. Increasing the ktup decreases the number of background hits. Not every word hit is investigated but instead initially looks for segment’s containing several nearby hits.

Name
FASTA (SOAP)
Documentation
http://www.ebi.ac.uk/Tools/webservices/services/sss/fasta_soap
Protocol
SOAP
WSDL
Endpoint
http://www.ebi.ac.uk/Tools/services/soap/fasta
Topic
Nucleotide Sequence Similarity, Protein Sequence Similarity
Type
Analysis
Tags
, , , , , , , , , ,
Description

FASTA (pronounced FAST-AYE) stands for FAST-All, reflecting the fact that it can be used for a fast protein comparison or [...]

Further information

FASTA (pronounced FAST-AYE) stands for FAST-All, reflecting the fact that it can be used for a fast protein comparison or a fast nucleotide comparison. This program achieves a high level of sensitivity for similarity searching at high speed. This is achieved by performing optimised searches for local alignments using a substitution matrix. The high speed of this program is achieved by using the observed pattern of word hits to identify potential matches before attempting the more time consuming optimised search. The trade-off between speed and sensitivity is controlled by the ktup parameter, which specifies the size of the word. Increasing the ktup decreases the number of background hits. Not every word hit is investigated but instead initially looks for segment’s containing several nearby hits.

Original source
BioCatalogue

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