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


BACKGROUND
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.
Prigent
V
V
Laboratoire de Biologie et Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, (CNRS/INSERM/ULP) BP 10142, 67404 Illkirch, Cedex, France. prigent@igbmc.u-strasbg.fr
Thierry
J C
JC
Poch
O
O
Plewniak
F
F
D000465:Algorithms; D000604:Amino Acyl-tRNA Synthetases / Q000737:chemistry* / Q000235:genetics*; D030562:Databases, Protein; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid; D012984:Software; D013329:Structure-Activity Relationship
D000604:Amino Acyl-tRNA Synthetases