BLASTX now uses composition based statistics (CBS).
BLASTX searches translate a nucleotide query and compare it to a protein database. BLASTX searches with CBS produce more reliable results. The increased accuracy is especially noticeable for query and subject sequences with biased compositions (i.e., low-complexity sequences). CBS has been available for some time with BLASTP, PSI-BLAST, and TBLASTN.
CBS is enabled by default for BLASTX searches at the NCBI BLAST website. CBS may be disabled by using the "Composition adjustment menu" in the Algorithm parameters part of the page. CBS will be available in the 2.2.27+ release of stand-alone BLASTX.
The CBS implementation for BLASTX is similar to that of TBLASTN, described at http://www.ncbi.nlm.nih.gov/pubmed/17156431
BLASTX searches translate a nucleotide query and compare it to a protein database. BLASTX searches with CBS produce more reliable results. The increased accuracy is especially noticeable for query and subject sequences with biased compositions (i.e., low-complexity sequences). CBS has been available for some time with BLASTP, PSI-BLAST, and TBLASTN.
CBS is enabled by default for BLASTX searches at the NCBI BLAST website. CBS may be disabled by using the "Composition adjustment menu" in the Algorithm parameters part of the page. CBS will be available in the 2.2.27+ release of stand-alone BLASTX.
The CBS implementation for BLASTX is similar to that of TBLASTN, described at http://www.ncbi.nlm.nih.gov/pubmed/17156431