DbW: automatic update of a functional family-specific multiple alignment
In: Bioinformatics Bioinformatics, Oxford University Press (OUP), 2005, 21 (8), pp.1437-42. ⟨10.1093/bioinformatics/bti218⟩; (2005-04-15)
Online
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Zugriff:
International audience; MOTIVATION: Recent advances in gene sequencing have provided complete sequence information for a number of genomes and as a result the amount of data in the sequence databases is growing at an exponential rate. We introduce here a new program, DbW, to automate the update of a functional family-specific multiple alignment that tries to include relevant sequences. The program is based on the use of different sources of information: sequences and annotations in databases. RESULTS: The advantages of DbW are demonstrated using the 20 families of aminoacyl-tRNA synthetases, where DbW detects a maximum of homologous sequences in the Swiss-Prot and SPTREMBL databases. The global specificity of DbW in this test is 98.4% (1.6% of the sequences included in the alignment did not belong to the family according to their function), and the global sensitivity of DbW is estimated to be 95.2%. Thus, DbW provides a reliable basis for the many applications that rely on accurate multiple alignments, e.g. functional residue identification, 2D/3D structure prediction or homology modeling. AVAILABILITY: The DbW software is available for download at ftp://ftp-igbmc.u-strasbg.fr/pub/DbW/DbW.tar and online at http://titus.u-strasbg.fr/DbW CONTACT: prigent@igbmc.u-strasbg.fr.
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DbW: automatic update of a functional family-specific multiple alignment
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Autor/in / Beteiligte Person: | Poch, Olivier ; Prigent, Veronique ; Thierry, Jean-Claude ; Plewniak, Frédéric ; Institut de génétique et biologie moléculaire et cellulaire (IGBMC) ; Université Louis Pasteur - Strasbourg I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS) |
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Quelle: | Bioinformatics Bioinformatics, Oxford University Press (OUP), 2005, 21 (8), pp.1437-42. ⟨10.1093/bioinformatics/bti218⟩; (2005-04-15) |
Veröffentlichung: | HAL CCSD, 2005 |
Medientyp: | unknown |
ISSN: | 1367-4803 (print) ; 1460-2059 (print) ; 1367-4811 (print) |
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