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    Please use this identifier to cite or link to this item: https://nccur.lib.nccu.edu.tw/handle/140.119/97941


    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
    Authors: 張家銘
    Floden, Evan;Tommaso, Paolo Di;Chatzou, Maria;Magis, Cedrik;Notredame, Cedric;Chang, Jia-Ming
    Contributors: 資科系
    Date: 2016-04
    Issue Date: 2016-06-16 12:06:14 (UTC+8)
    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.
    Relation: Nucleic Acids Research, 2016
    Data Type: article
    DOI link: http://dx.doi.org/10.1093/nar/gkw300
    DOI: 10.1093/nar/gkw300
    Appears in Collections:[Department of Computer Science ] Periodical Articles

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