CS-BLAST

CS-BLAST
Developer(s) Angermueller C, Biegert A, and Soeding J
Stable release 2.2.3 / December 7, 2013 (2013-12-07)
Preview release 1.1 / April 14, 2009 (2009-04-14)
Written in C++
Available in English
Type Bioinformatics tool
License GNU GPL v3
Website ftp://toolkit.genzentrum.lmu.de/pub/csblast/, https://github.com/cangermueller/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

References

  1. 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.
  2. ↑ 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.
  3. ↑ "Better Sequence Searches Of Genes And Proteins Devised". ScienceDaily. Mar 7, 2009. Retrieved 2009-08-14.
  4. ↑ 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.
  5. ↑ 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


This article is issued from Wikipedia - version of the Sunday, November 02, 2014. The text is available under the Creative Commons Attribution/Share Alike but additional terms may apply for the media files.