AAT (analysis and annotation tool) includes two sets of programs, one set (DPS/NAP) for comparing the query sequence with a protein database, and the other (DDS/GAP2) for comparing the query with a cDNA database (Huang et al., 1997). Each set contains a fast database search program and a rigorous alignment program. The database search program quickly identifies regions of the query sequence that are similar to a database sequence. Then the alignment program constructs an optimal alignment for each region and the database sequence. The alignment program also reports the coordinates of exons in the query sequence.
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Huang, X., Adams, M.D., Zhou, H. and Kerlavage, A.R. (1997).
A tool for analyzing and annotating genomic sequences, Genomics 46, 37-45.