PHOG-BLAST--a new generation tool for fast similarity search of protein families.

ABSTRACT:

Background

The need to compare protein profiles frequently arises in various protein research areas: comparison of protein families, domain searches, resolution of orthology and paralogy. The existing fast algorithms can only compare a protein sequence with a protein sequence and a profile with a sequence. Algorithms to compare profiles use dynamic programming and complex scoring functions.

Results

We developed a new algorithm called PHOG-BLAST for fast similarity search of profiles. This algorithm uses profile discretization to convert a profile to a finite alphabet and utilizes hashing for fast search. To determine the optimal alphabet, we analyzed columns in reliable multiple alignments and obtained column clusters in the 20-dimensional profile space by applying a special

SUBMITTER: Merkeev IV 

PROVIDER: S-EPMC1522020 | biostudies-literature | 2006 Jun

REPOSITORIES: biostudies-literature