Significant speedup of database searches with HMMs by search space reduction with PSSM family models.

ABSTRACT:

Motivation

Profile hidden Markov models (pHMMs) are currently the most popular modeling concept for protein families. They provide sensitive family descriptors, and sequence database searching with pHMMs has become a standard task in today's genome annotation pipelines. On the downside, searching with pHMMs is computationally expensive.

Results

We propose a new method for efficient protein family classification and for speeding up database searches with pHMMs as is necessary for large-scale analysis scenarios. We employ simpler models of protein families called position-specific scoring matrices family models (PSSM-FMs). For fast database search, we combine full-text indexing, efficient exact p-value computation of PSSM match scores and fast fragment chaining. The resulting

SUBMITTER: Beckstette M 

PROVIDER: S-EPMC2788931 | biostudies-literature | 2009 Dec

REPOSITORIES: biostudies-literature