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PSI/TM-Coffee: a web server for fast and accurate multiple sequence alignments of regular and transmembrane proteins using homology extension on reduced databases

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dc.contributor.author Floden, Evan Wade
dc.contributor.author Tommaso, Paolo Di
dc.contributor.author Chatzou, Maria, 1985-
dc.contributor.author Magis, Cedrik
dc.contributor.author Notredame, Cedric
dc.contributor.author Chang, Jia-Ming, 1978-
dc.date.accessioned 2017-01-25T07:49:12Z
dc.date.available 2017-01-25T07:49:12Z
dc.date.issued 2016
dc.identifier.citation Floden EW, Tommaso PD, Chatzou M, Magis C, Notredame C, Chang J-M. PSI/TM-Coffee: a web server for fast and accurate multiple sequence alignments of regular and transmembrane proteins using homology extension on reduced databases. Nucleic Acids Research. 2016; 44(W1): W339-343. DOI: 10.1093/nar/gkw300
dc.identifier.issn 0305-1048
dc.identifier.uri http://hdl.handle.net/10230/27980
dc.description.abstract The PSI/TM-Coffee web server performs multiple sequence alignment (MSA) of proteins by combining homology extension with a consistency based alignment approach. Homology extension is performed with Position Specific Iterative (PSI) BLAST searches against a choice of redundant and non-redundant databases. The main novelty of this server is to allow databases of reduced complexity to rapidly perform homology extension. This server also gives the possibility to use transmembrane proteins (TMPs) reference databases to allow even faster homology extension on this important category of proteins. Aside from an MSA, the server also outputs topological prediction of TMPs using the HMMTOP algorithm. Previous benchmarking of the method has shown this approach outperforms the most accurate alignment methods such as MSAProbs, Kalign, PROMALS, MAFFT, ProbCons and PRALINE™. The web server is available at http://tcoffee.crg.cat/tmcoffee.
dc.description.sponsorship This work was supported by Plan Nacional [BFU2011-28575 to C.N., P.D.]; Center for Genomic Regulation (CRG); ‘Fundació Obra Social la Caixa’ (to E.W.F, M.C); Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013–2017’ [SEV-2012–0208]; Center for Genomic Regulation (CRG).
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher Oxford University Press
dc.relation.ispartof Nucleic Acids Research. 2016; 44(W1): W339-343
dc.rights © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited.
dc.rights.uri http://creativecommons.org/licenses/by-nc/4.0/
dc.title PSI/TM-Coffee: a web server for fast and accurate multiple sequence alignments of regular and transmembrane proteins using homology extension on reduced databases
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1093/nar/gkw300
dc.subject.keyword Coffee
dc.subject.keyword Benchmarking
dc.subject.keyword Sequence alignment
dc.subject.keyword Integral membrane proteins
dc.subject.keyword Basic local alignment search tool
dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/BFU2011-28575
dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/SEV2012–0208
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion


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