Refining multiple sequence alignments with conserved core regions

被引：26

作者：

Chakrabarti, Saikat ^{[1
]}

Lanczycki, Christopher J. ^{[1
]}

Panchenko, Anna R. ^{[1
]}

Przytycka, Teresa M. ^{[1
]}

Thiessen, Paul A. ^{[1
]}

Bryant, Stephen H. ^{[1
]}

机构：

[1] Natl Lib Med, Natl Ctr Biotechnol Informat, NIH, Bethesda, MD 20894 USA

来源：

NUCLEIC ACIDS RESEARCH | 2006年 / 34卷 / 09期

基金：

美国国家卫生研究院;

关键词：

D O I：

10.1093/nar/gkl274

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：2598 / 2606

页数：9

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