CORAL: aligning conserved core regions across domain families.

ABSTRACT:

Motivation

Homologous protein families share highly conserved sequence and structure regions that are frequent targets for comparative analysis of related proteins and families. Many protein families, such as the curated domain families in the Conserved Domain Database (CDD), exhibit similar structural cores. To improve accuracy in aligning such protein families, we propose a profile-profile method CORAL that aligns individual core regions as gap-free units.

Results

CORAL computes optimal local alignment of two profiles with heuristics to preserve continuity within core regions. We benchmarked its performance on curated domains in CDD, which have pre-defined core regions, against COMPASS, HHalign and PSI-BLAST, using structure superpositions and comprehensive curator-optimiz

SUBMITTER: Fong JH 

PROVIDER: S-EPMC2712342 | biostudies-literature | 2009 Aug

REPOSITORIES: biostudies-literature