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Updated: Aug 20, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
Published on: July 14, 2015
DbW: automatic update of a functional family-specific multiple alignment
V Prigent1, J C Thierry, O Poch
1Laboratoire 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
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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