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©Oxford University Press

Visual BLAST and Visual FASTA: graphic workbenches for interactive analysis of full BLAST and FASTA outputs under Microsoft Windows 95/NT

P. Durand 1, L. Canard and J.P. Mornon

Systémes Moleéculaires er Biologie Structurale. Laboratoire de Mineéralogie- Cristallographie, CNRS URA09, Universités Paris VI-Paris VII. T16, case 115.4 Place Jussieu F-75252 Paris Cedex 5, France

1To whom correspondence should be addressed

MOTIVATION:: When routinely analysing protein sequences, detailed analysis of database search results made with BLAST and FASTA becomes exceedingly time consuming and tedious work, as the resultant file may contain 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 within BLAST and FASTA output jiles makes them diflcult to read.

RESULTS:: To facilitate and accelerate this analysis, we present, for the first time, two easy-to-use programs designed for interactive analysis of full BLAST and FASTA output files containing protein sequence alignments. The programs, Visual BLAST and Visual FASTA, run under Microsoft Windows 95 or NT systems They are based on the same intuitive graphical user interjiace (GUI) with extensive viewing, searching, editing, printing and multithreading capabilities. These programs improve the browsing of BLAST/FASTA results by offering a more convenient presentation of these results. They also implement on a computer several analytical tools which automate a manual methodology used for detailed analysis of BLAST and FASTA outputs These tools include a painvise sequence alignment viewer, a Hydrophobic Cluster Analysis plot alignment viewer and a tool displaying a graphical map of all database sequences aligned with the query sequence.In addition, Visual Blast includes tools for multiple sequence alignment analysis (with an amino acid patterns search engine), and Visual FASTA provides a GUI to the FASTA program.

AVAILABILITY:: The programs are freely available on the Web (http://www.lmcp.jussieu.fr/{small tilde}durand).

CONTACT:: E-mail: durand{at}lmcp.jussieu.fr

Received on November 25, 1996; revised on January 29, 1997; accepted on January 30, 1997

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