Match-Box_server: a multiple sequence alignment tool placing emphasis on reliability
Department of Biology, Facultes Universitaires Notre-Dame de la Paix 61 rue de Bruxelles, B-5000 Namur, Belgium
1 To whom correspondence should be addressed
Motivation: The Match-Box software comprises protein sequence alignment tools based on strict statistical thresholds of similarity between protein segments. The method circumvents the gap penalty requirement: gaps being the result of the alignment and not a governing parameter of the procedure. The reliable conserved regions outlined by Match-Box are particularly relevant for homology modelling of protein structures, prediction of essential residues for sitedirected mutagenesis and oligonucleotide design for cloning homologous genes by polymerase chain reaction (PCR).
Results: The method produces reliable results, as assessed by tests performed on protein families of known structures and of low sequence similarity. A reliability score is computed in relation to a threshold of similarity progressively raised to extend the aligned regions to their maximal length, up to the significance limit of matching segments. The score obtained at each position is printed below the sequences and allows a discriminant reading of each aligned region.
Availability: Sequences may be submitted to a Web server at http://www.fundp.ac.be/sciences/biologie/bms/matchbox_submit.html or sent by e-mail to matchbox{at}biq.fundp.ac.be (help available by just mailing help).
Received on September 9, 1996; revised on December 4, 1996; accepted on December 10, 1996
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