Simple adjustment of the sequence weight algorithm remarkably enhances PSI-BLAST performance.

ABSTRACT:

Background

PSI-BLAST, an extremely popular tool for sequence similarity search, features the utilization of Position-Specific Scoring Matrix (PSSM) constructed from a multiple sequence alignment (MSA). PSSM allows the detection of more distant homologs than a general amino acid substitution matrix does. An accurate estimation of the weights for sequences in an MSA is crucially important for PSSM construction. PSI-BLAST divides a given MSA into multiple blocks, for which sequence weights are calculated. When the block width becomes very narrow, the sequence weight calculation can be odd.

Results

We demonstrate that PSI-BLAST indeed generates a significant fraction of blocks having width less than 5, thereby degrading the PSI-BLAST performance. We revised the code of PSI-BLAST

SUBMITTER: Oda T 

PROVIDER: S-EPMC5455086 | biostudies-literature | 2017 Jun

REPOSITORIES: biostudies-literature