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

V. Prigent (1) , J. Thierry (1) , O. Poch (1) , F. Plewniak (1)

1 IGBMC - Institut de génétique et biologie moléculaire et cellulaire

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

Domaines: Génétique

V. Prigent, J. Thierry, O. Poch, F. Plewniak. DbW: automatic update of a functional family-specific multiple alignment. Bioinformatics, 2004, 21 (8), pp.1437-1442. ⟨10.1093/bioinformatics/bti218⟩. ⟨hal-04542626⟩