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RE-MuSiC: a tool for multiple sequence alignment with regular expression constraints

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 des...

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Detalles Bibliográficos
Autores principales: Chung, Yun-Sheng, Lee, Wei-Hsun, Tang, Chuan Yi, Lu, Chin Lung
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2007
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933182/
https://www.ncbi.nlm.nih.gov/pubmed/17488842
http://dx.doi.org/10.1093/nar/gkm275
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author Chung, Yun-Sheng
Lee, Wei-Hsun
Tang, Chuan Yi
Lu, Chin Lung
author_facet Chung, Yun-Sheng
Lee, Wei-Hsun
Tang, Chuan Yi
Lu, Chin Lung
author_sort Chung, Yun-Sheng
collection PubMed
description 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.
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spelling pubmed-19331822007-07-31 RE-MuSiC: a tool for multiple sequence alignment with regular expression constraints Chung, Yun-Sheng Lee, Wei-Hsun Tang, Chuan Yi Lu, Chin Lung Nucleic Acids Res Articles 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. Oxford University Press 2007-07 2007-05-08 /pmc/articles/PMC1933182/ /pubmed/17488842 http://dx.doi.org/10.1093/nar/gkm275 Text en © 2007 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Articles
Chung, Yun-Sheng
Lee, Wei-Hsun
Tang, Chuan Yi
Lu, Chin Lung
RE-MuSiC: a tool for multiple sequence alignment with regular expression constraints
title RE-MuSiC: a tool for multiple sequence alignment with regular expression constraints
title_full RE-MuSiC: a tool for multiple sequence alignment with regular expression constraints
title_fullStr RE-MuSiC: a tool for multiple sequence alignment with regular expression constraints
title_full_unstemmed RE-MuSiC: a tool for multiple sequence alignment with regular expression constraints
title_short RE-MuSiC: a tool for multiple sequence alignment with regular expression constraints
title_sort re-music: a tool for multiple sequence alignment with regular expression constraints
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933182/
https://www.ncbi.nlm.nih.gov/pubmed/17488842
http://dx.doi.org/10.1093/nar/gkm275
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