CS-BLAST an improved version of BLAST (Basic Local Alignment Search Tool)

BLAST

In bioinformatics, Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences...

, is a program for protein

Protein

Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...

 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.

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. 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

Position-specific scoring matrix

A position weight matrix , also called position-specific weight matrix or position-specific scoring matrix , is a commonly used representation of motifs in biological sequences....

 is also available. This program (CSI-BLAST) is similar to the popular PSI-BLAST

BLAST

In bioinformatics, Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences...

(position-specific iterative BLAST) program. Two search iterations of CSI-BLAST are more sensitive than five search iterations of PSI-BLAST.