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Journal Articles Bioinformatics Year : 2005

DbW: automatic update of a functional family-specific multiple alignment.

Abstract

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.

Dates and versions

hal-00187728 , version 1 (15-11-2007)

Identifiers

Cite

V. Prigent, J. C. Thierry, O. Poch, F. Plewniak. DbW: automatic update of a functional family-specific multiple alignment.. Bioinformatics, 2005, 21 (8), pp.1437-42. ⟨10.1093/bioinformatics/bti218⟩. ⟨hal-00187728⟩
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