Refining multiple sequence alignments with conserved core regions.

ABSTRACT: Accurate multiple sequence alignments of proteins are very important to several areas of computational biology and provide an understanding of phylogenetic history of domain families, their identification and classification. This article presents a new algorithm, REFINER, that refines a multiple sequence alignment by iterative realignment of its individual sequences with the predetermined conserved core (block) model of a protein family. Realignment of each sequence can correct misalignments between a given sequence and the rest of the profile and at the same time preserves the family's overall block model. Large-scale benchmarking studies showed a noticeable improvement of alignment after refinement. This can be inferred from the increased alignment score and enhanced sensitivity for data

SUBMITTER: Chakrabarti S 

PROVIDER: S-EPMC1463900 | biostudies-literature | 2006

REPOSITORIES: biostudies-literature