Composition-based statistics and translated nucleotide searches: improving the TBLASTN module of BLAST.

ABSTRACT:

Background

TBLASTN is a mode of operation for BLAST that aligns protein sequences to a nucleotide database translated in all six frames. We present the first description of the modern implementation of TBLASTN, focusing on new techniques that were used to implement composition-based statistics for translated nucleotide searches. Composition-based statistics use the composition of the sequences being aligned to generate more accurate E-values, which allows for a more accurate distinction between true and false matches. Until recently, composition-based statistics were available only for protein-protein searches. They are now available as a command line option for recent versions of TBLASTN and as an option for TBLASTN on the NCBI BLAST web server.

Results

We evaluate the stat

SUBMITTER: Gertz EM 

PROVIDER: S-EPMC1779365 | biostudies-literature | 2006 Dec

REPOSITORIES: biostudies-literature