標題: RE-MuSiC: a tool for multiple sequence alignment with regular expression constraints
作者: Chung, Yun-Sheng
Lee, Wei-Hsun
Tang, Chuan Yi
Lu, Chin Lung
生物科技學系
生物資訊及系統生物研究所
Department of Biological Science and Technology
Institude of Bioinformatics and Systems Biology
公開日期: 1-七月-2007
摘要: RE-MuSiC is a web-based multiple sequence alignment tool that can incorporate biological knowledge about structure, function, or conserved patterns regarding the sequences of interest. It accepts amino acid or nucleic acid sequences and a set of constraints as inputs. The constraints are pattern descriptions, instead of exact positions of fragments to be aligned together. The output is an alignment where for each pattern (constraint), an occurrence on each sequence can be found aligned together with those on the other sequences, in a manner that the overall alignment is optimized. Its predecessor, MuSiC, has been found useful by researchers since its release in 2004. However, it is noticed in applications that the pattern formulation adopted in MuSiC, namely, plain strings allowing mismatches, is not expressive and flexible enough. The constraint formulation adopted in RE-MuSiC is therefore enhanced to be regular expressions, which is convenient in expressing many biologically significant patterns like those collected in the PROSITE database, or structural consensuses that often involve variable ranges between conserved parts. Experiments demonstrate that RE-MuSiC can be used to help predict important residues and locate phylogenetically conserved structural elements. RE-MuSiC is available on-line at http://140.113.239.131/RE-MUSIC.
URI: http://dx.doi.org/10.1093/nar/gkm275
http://hdl.handle.net/11536/10621
ISSN: 0305-1048
DOI: 10.1093/nar/gkm275
期刊: NUCLEIC ACIDS RESEARCH
Volume: 35
Issue: 
起始頁: W639
結束頁: W644
顯示於類別:期刊論文


文件中的檔案:

  1. 000255311500118.pdf