VISUAL BLAST AND VISUAL FASTA - GRAPHIC WORKBENCHES FOR INTERACTIVE ANALYSIS OF FULL BLAST AND FASTA OUTPUTS UNDER MICROSOFT WINDOWS-95 WINDOWS-NT/

Motivation: When routinely analysing protein sequences, detailed analy sis of database search results made with BLAST and FASTA becomes excee dingly time consuming and tedious work, as the resultant file may cont ain a list of hundreds of potential homologies. The interpretation of these results is usually carried out with a text editor which is not a convenient tool for this analysis, In addition, the format of data wi thin BLAST and FASTA output files makes them difficult to read. Result s: To facilitate and accelerate this analysis, we present, for the fir st time, two easy-to-use programs designed for interactive analysis of full BLAST and FASTA output files containing protein sequence alignme nts. The programs, Visual BLAST and Visual FASTA, run under Microsoft Windows 95 or NT systems. They are based on the same intuitive graphic al user interface (GUI) with extensive viewing, searching, editing, pr inting and multithreading capabilities. These programs improve the bro wsing of BLAST/FASTA results by offering a more convenient presentatio n of these results. They also implement on a computer several analytic al tools which automate a manual methodology used for detailed analysi s of BLAST and FASTA outputs. These tools include a pairwise sequence alignment viewer, a Hydrophobic Cluster Analysis plot alignment viewer and a tool displaying a graphical map of all database sequences align ed with the query sequence. In addition, Visual Blast includes tools f or multiple sequence alignment analysis (with an amino acid patterns s earch engine), and Visual FASTA provides a GUI to the FASTA program.