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 Wadeca
• dc.contributor.author Tommaso, Paolo Dica
• dc.contributor.author Chatzou, Maria, 1985-ca
• dc.contributor.author Magis, Cedrikca
• dc.contributor.author Notredame, Cedricca
• dc.contributor.author Chang, Jia-Ming, 1978-ca
• dc.date.accessioned 2017-01-25T07:49:12Z
• dc.date.available 2017-01-25T07:49:12Z
• dc.date.issued 2016ca
• 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/pdfca
• 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):339-43. DOI: 10.1093/nar/gkw300ca
• dc.identifier.doi http://dx.doi.org/10.1093/nar/gkw300
• dc.identifier.issn 0305-1048ca
• dc.identifier.uri http://hdl.handle.net/10230/27980
• dc.language.iso engca
• dc.publisher Oxford University Pressca
• dc.relation.ispartof Nucleic Acids Research. 2016;44(W1):339-43
• dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/BFU2011-28575
• dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/SEV2012–0208
• 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.ca
• dc.rights.accessRights info:eu-repo/semantics/openAccessca
• dc.rights.uri http://creativecommons.org/licenses/by-nc/4.0/
• 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.title PSI/TM-Coffee: a web server for fast and accurate multiple sequence alignments of regular and transmembrane proteins using homology extension on reduced databasesca
• dc.type info:eu-repo/semantics/articleca
• dc.type.version info:eu-repo/semantics/publishedVersionca