SAW - A GRAPHICAL USER-INTERFACE FOR THE ANALYSIS OF IMMUNOGLOBULIN VARIABLE DOMAIN SEQUENCES

The Sequence Analysis Workshop (SAW) is an interactive program for seq uence analysis of immunoglobulin variable domains. Sequences for SAW c an be obtained from GenBank(R) or from a standard text file. SAW can c ompare a variable domain to as many as 100 different sequences, calcul ate the extent of homology, sort the sequences by their degree o simil arity, translate the nucleotide codons into amino acids and then displ ay the results in either a graphical or text format. These comparisons allow the investigator to determine the likely germ-line progenitors of a variable domain and to visualize how it differs from other antibo dy genes by functional region. SAW supports replacement and silent sit e substitution analysis by either codon or region, thus providing rapi d insight into the forces that have shaped mutations. The sequence com parisons can be printed out as an aid for paper analysis or for prepar ation of figures for publication. SAW is written in Microsoft(R) C for use with the Microsoft Windows(TM) graphics environment. The use of c olor and graphics, the generation of subsidiary windows that contain t he results of specific analyses and the mouse-driven control of the pr ogram make SAW an easy-to-use tool for immunoglobulin sequence compari son.