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題名 Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures 作者 Chang, Jia-Ming
張家銘
Notredame, Cedric
Kemena, Carsten
Jose, Espinosa-Carrasco
Erb, Ionas
Tommaso, Paolo Di
Bussotti, Giovanni
Magis, Cedrik
Jean-Francois
Taly貢獻者 資科系 日期 2011-11 上傳時間 27-四月-2016 15:30:09 (UTC+8) 摘要 T-Coffee (Tree-based consistency objective function for alignment evaluation) is a versatile multiple sequence alignment (MSA) method suitable for aligning most types of biological sequences. The main strength of T-Coffee is its ability to combine third party aligners and to integrate structural (or homology) information when building MSAs. The series of protocols presented here show how the package can be used to multiply align proteins, RNA and DNA sequences. The protein section shows how users can select the most suitable T-Coffee mode for their data set. Detailed protocols include T-Coffee, the default mode, M-Coffee, a meta version able to combine several third party aligners into one, PSI (position-specific iterated)-Coffee, the homology extended mode suitable for remote homologs and Expresso, the structure-based multiple aligner. We then also show how the T-RMSD (tree based on root mean square deviation) option can be used to produce a functionally informative structure-based clustering. RNA alignment procedures are described for using R-Coffee, a mode able to use predicted RNA secondary structures when aligning RNA sequences. DNA alignments are illustrated with Pro-Coffee, a multiple aligner specific of promoter regions. We also present some of the many reformatting utilities bundled with T-Coffee. The package is an open-source freeware available from http://www.tcoffee.org/. 關聯 Nature Protocols, 6, 1669-1682 資料類型 article DOI http://dx.doi.org/10.1038/nprot.2011.393 dc.contributor 資科系 - dc.creator (作者) Chang, Jia-Ming - dc.creator (作者) 張家銘 zh_TW dc.creator (作者) Notredame, Cedric en_US dc.creator (作者) Kemena, Carsten en_US dc.creator (作者) Jose, Espinosa-Carrasco en_US dc.creator (作者) Erb, Ionas en_US dc.creator (作者) Tommaso, Paolo Di en_US dc.creator (作者) Bussotti, Giovanni en_US dc.creator (作者) Magis, Cedrik en_US dc.creator (作者) Jean-Francois en_US dc.creator (作者) Taly en_US dc.date (日期) 2011-11 - dc.date.accessioned 27-四月-2016 15:30:09 (UTC+8) - dc.date.available 27-四月-2016 15:30:09 (UTC+8) - dc.date.issued (上傳時間) 27-四月-2016 15:30:09 (UTC+8) - dc.identifier.uri (URI) http://nccur.lib.nccu.edu.tw/handle/140.119/86639 - dc.description.abstract (摘要) T-Coffee (Tree-based consistency objective function for alignment evaluation) is a versatile multiple sequence alignment (MSA) method suitable for aligning most types of biological sequences. The main strength of T-Coffee is its ability to combine third party aligners and to integrate structural (or homology) information when building MSAs. The series of protocols presented here show how the package can be used to multiply align proteins, RNA and DNA sequences. The protein section shows how users can select the most suitable T-Coffee mode for their data set. Detailed protocols include T-Coffee, the default mode, M-Coffee, a meta version able to combine several third party aligners into one, PSI (position-specific iterated)-Coffee, the homology extended mode suitable for remote homologs and Expresso, the structure-based multiple aligner. We then also show how the T-RMSD (tree based on root mean square deviation) option can be used to produce a functionally informative structure-based clustering. RNA alignment procedures are described for using R-Coffee, a mode able to use predicted RNA secondary structures when aligning RNA sequences. DNA alignments are illustrated with Pro-Coffee, a multiple aligner specific of promoter regions. We also present some of the many reformatting utilities bundled with T-Coffee. The package is an open-source freeware available from http://www.tcoffee.org/. - dc.format.extent 107 bytes - dc.format.mimetype text/html - dc.relation (關聯) Nature Protocols, 6, 1669-1682 - dc.title (題名) Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures - dc.type (資料類型) article - dc.identifier.doi (DOI) 10.1038/nprot.2011.393 - dc.doi.uri (DOI) http://dx.doi.org/10.1038/nprot.2011.393 -
