Composition-modified matrices improve identification of homologs of saccharomyces cerevisiae low-complexity glycoproteins.

ABSTRACT: Yeast glycoproteins are representative of low-complexity sequences, those sequences rich in a few types of amino acids. Low-complexity protein sequences comprise more than 10% of the proteome but are poorly aligned by existing methods. Under default conditions, BLAST and FASTA use the scoring matrix BLOSUM62, which is optimized for sequences with diverse amino acid compositions. Because low-complexity sequences are rich in a few amino acids, these tools tend to align the most common residues in nonhomologous positions, thereby generating anomalously high scores, deviations from the expected extreme value distribution, and small e values. This anomalous scoring prevents BLOSUM62-based BLAST and FASTA from identifying correct homologs for proteins with low-complexity sequences, including Sac

SUBMITTER: Coronado JE 

PROVIDER: S-EPMC1459670 | biostudies-literature | 2006 Apr

REPOSITORIES: biostudies-literature