title: 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 database searching using the sequence profiles derived from refined alignments compared with the original alignments. A standalone version of the program is available by ftp distribution (ftp://ftp.ncbi.nih.gov/pub/REFINER) and will be incorporated into the next release of the Cn3D structure/alignment viewer.
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
authors.forename: Saikat
authors.initials: S
authors.lastname: Chakrabarti
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Lanczycki
authors.forename: Anna R
authors.initials: AR
authors.lastname: Panchenko
authors.forename: Teresa M
authors.initials: TM
authors.lastname: Przytycka
authors.forename: Paul A
authors.initials: PA
authors.lastname: Thiessen
authors.forename: Stephen H
authors.initials: SH
authors.lastname: Bryant
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D017124:Conserved Sequence; D020407:Internet; D008969:Molecular Sequence Data; D011786:Quality Control; D015203:Reproducibility of Results; D016415:Sequence Alignment / Q000379:methods* / Q000592:standards; D020539:Sequence Analysis, Protein / Q000379:methods* / Q000592:standards