CS-BLAST

CS-BLAST
Developer(s) Andreas Biegert and Johannes Soeding
Stable release 1.03 / April 14, 2009; 2 years ago (2009-04-14)
Preview release 1.1 / April 14, 2009; 2 years ago (2009-04-14)
Written in C++
Available in English
Type Bioinformatics tool
License Creative Commons Attribution-NonCommercial-3.0
Website ftp://toolkit.lmb.uni-muenchen.de/csblast/

CS-BLAST (context-specific BLAST), an improved version[1] of BLAST (Basic Local Alignment Search Tool),[2] is a program for protein sequence searching.

Sequence searches are frequently performed by biologists to infer the function of an unknown protein from its sequence. For this purpose, the protein's sequence is compared to the sequences of millions of other protein sequences in public databases. The functions of the protein can often be inferred from the functions of the most similar sequences found in such a search.[3]

Contents

Implementation

CS-BLAST is implemented as a wrapper around BLAST. It finds up to twice as many distantly related protein sequences as BLAST at the same speed and error rate.[4] This is achieved by considering the letters that make up protein sequences, the amino acids, in the context of the 12 neighboring amino acids (six on either side). Whereas the probabilities for amino acids to mutate into other types of amino acids in related proteins depend only on the single amino acid in BLAST and other sequence search programs, mutation probabilities in CS-BLAST depend on the local sequence contexts.

An extension of CS-BLAST for iterative search with position-specific scoring matrices is also available. This program (CSI-BLAST) is similar to the popular PSI-BLAST (position-specific iterative BLAST) program.[5] Two search iterations of CSI-BLAST are more sensitive than five search iterations of PSI-BLAST.[4]

See also

References

  1. ^ "Better Sequence Searches Of Genes And Proteins Devised". ScienceDaily. Mar. 7, 2009. http://www.sciencedaily.com/releases/2009/02/090223131125.htm. Retrieved 2009-08-14. 
  2. ^ 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. 
  3. ^ Davison DB (2002). 3. "An overview of sequence similarity ("homology") searching". Curr Protoc Bioinformatics Chapter 3: Unit 3.1. doi:10.1002/0471250953.bi0301s00. PMID 18792936. 
  4. ^ a b Biegert A, Soeding J (2009). "Sequence context-specific profiles for homology searching". Proc Natl Acad Sci USA 106 (10): 3770–3775. doi:10.1073/pnas.0810767106. PMC 2645910. PMID 19234132. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2645910. 
  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. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=146917. 

External links