A TOOL FOR ANALYZING AND ANNOTATING GENOMIC SEQUENCES

We describe a tool for analyzing and annotating large genomic sequence s containing introns. The analysis and annotation tool (AAT) includes two sets of programs, one for comparing the query sequence with a prot ein database and the other for comparing the query with a cDNA databas e. Each set contains a fast database search program and a rigorous ali gnment program. The database search program quickly identifies regions of the query sequence that are similar to a database sequence. Then t he alignment program constructs an optimal alignment for each region a nd the database sequence. The alignment program also reports the coord inates of exons in the query sequence. Pairwise alignments of the quer y sequence with protein and cDNA database sequences are combined into multiple sequence alignments, which provide a view of all protein and cDNA sequences matching a query region. On a data set of 570 DNA seque nces, AAT identified 94% of coding nucleotides correctly and 74% of ex ons exactly. Results of analyzing a human BAC sequence with the AAT to ol are also presented. The AAT tool reduces the labor-intensive work o f locating the exons of the query sequence and improves the process of defining intron-exon boundaries by using the wealth of available prot ein and cDNA data. (C) 1997 Academic Press.