MATCH-BOX-SERVER - A MULTIPLE SEQUENCE ALIGNMENT TOOL PLACING EMPHASIS ON RELIABILITY

Motivation: The Match-Box software comprises protein sequence alignmen t tools based on strict statistical thresholds of similarity between p rotein segments. The method circum vents the gap penalty requirement: gaps being the result of the alignment and not a governing parameter o f the procedure. The reliable conserved regions outlined by Match-Box are particularly relevant for homology modelling of protein structures , prediction of essential residues for site-directed mutagenesis and o ligonucleotide design for cloning homologous genes by polymerase chain reaction (PCR). Results: The method produces reliable results, as ass essed by rests performed on protein families of known structures and o f low sequence similarity. A reliability score is computed in relation to a threshold of similarity progressively raised to extend the align ed regions to their maximal length, up to the significance limit of ma tching 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 sewer at p.ac.be/s ciences/biologie/bms/matchbox_submit.html or sent by e-mail to matchbo x@biq.fundp.ac.be (help available by just mailing help).