Consensus sequences improve PSI-BLAST through mimicking profile-profile alignments.

ABSTRACT: Sequence alignments may be the most fundamental computational resource for molecular biology. The best methods that identify sequence relatedness through profile-profile comparisons are much slower and more complex than sequence-sequence and sequence-profile comparisons such as, respectively, BLAST and PSI-BLAST. Families of related genes and gene products (proteins) can be represented by consensus sequences that list the nucleic/amino acid most frequent at each sequence position in that family. Here, we propose a novel approach for consensus-sequence-based comparisons. This approach improved searches and alignments as a standard add-on to PSI-BLAST without any changes of code. Improvements were particularly significant for more difficult tasks such as the identification of distant structu

SUBMITTER: Przybylski D 

PROVIDER: S-EPMC1874647 | biostudies-literature | 2007

REPOSITORIES: biostudies-literature