CS-BLAST
Developer(s) | Angermueller C, Biegert A, and Soeding J |
---|---|
Stable release |
2.2.3
/ December 7, 2013 |
Preview release |
1.1
/ April 14, 2009 |
Written in | C++ |
Available in | English |
Type | Bioinformatics tool |
License | GNU GPL v3 |
Website | http://wwwuser.gwdg.de/~compbiol/data/csblast/releases/, https://github.com/soedinglab/csblast |
CS-BLAST [1] [2] [3] (Context-Specific BLAST) is a protein sequence search tools that extends BLAST (Basic Local Alignment Search Tool),[4] (Basic Local Alignment Search Tool) by context-specific mutation probabilities. CSI-BLAST (Context-Specific Iterated) BLAST is the context-specific analog of PSI-BLAST [5] (Position-Specific Iterated) BLAST. CS-BLAST and CSI-BLAST are available as web-server and can be downloaded freely .
Method
For aligning two protein sequences, BLAST uses substitution matrix mutation probabilities which only depend on a single amino-acid. The mutation probabilities of an amino-acid, however, are constrained by its structural context: a lysine in an amphipathic alpha helix stabilizes the protein structure and is less likely to mutate than a lysine in a disordered region. CS-BLAST predicts context-specific mutation probabilities that depend on 13 amino acids (the central amino acid and twelve neighboring amino acids). Context-specific mutation probabilities are more accurate than substitution matrix probabilities and improve sequence alignments as well as sequence searching.
Performance
CS-BLAST finds 50% more homologous protein sequences than BLAST at the same error rate and with a negligible runtime overhead. CS-BLAST alignments are more sensitive and more precise than BLAST alignments, in particular for sequences with a sequence identity below 30%. CSI-BLAST finds with two search iterations more protein sequences than PSI-BLAST with five search iterations.[1]
See also
- Sequence alignment software
- Multiple sequence alignment
- Position-specific scoring matrix
- BLAST (Basic Local Alignment Search Tool)
- HH-suite software package
References
- 1 2 Angermüller, C.; Biegert, A.; Söding, J. (Dec 2012). "Discriminative modelling of context-specific amino acid substitution probabilities.". Bioinformatics. 28 (24): 3240–7. doi:10.1093/bioinformatics/bts622. PMID 23080114.
- ↑ Biegert, A.; Söding, J. (Mar 2009). "Sequence context-specific profiles for homology searching.". Proc Natl Acad Sci U S A. 106 (10): 3770–5. doi:10.1073/pnas.0810767106. PMC 2645910. PMID 19234132.
- ↑ "Better Sequence Searches Of Genes And Proteins Devised". ScienceDaily. Mar 7, 2009. Retrieved 2009-08-14.
- ↑ Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990). "Basic local alignment search tool.". J Mol Biol. 215 (3): 403–410. doi:10.1016/S0022-2836(05)80360-2. PMID 2231712.
- ↑ Altschul SF; Madden TL; Schäffer AA; Zhang J; Zhang Z; Miller W; Lipman DJ. (1997). "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.". Nucleic Acids Res. 25 (17): 3389–3402. doi:10.1093/nar/25.17.3389. PMC 146917. PMID 9254694.
External links
- CS-BLAST — free server at University of Munich (LMU)
- CS-BLAST — free server at Max-Planck Institute in Tuebingen
- CS-BLAST source code