A New Fast Tool for Aligning Proteins with Genome and Accurately Reconstructing Exon-intron Gene Structure

ProtMap program maps a set of protein sequences to a genomic sequence, producing gene structures and corresponding alignments of coding exons with the similar or identical protein queries. ProtMap uses a genomic sequence and a set of protein sequences as its input data, and reconstructs gene structure based on protein identity or homology, in contrast to a set of unordered alignment fragments generated by Blast. The program is very fast, and it produces gene structures similar to those of Genewise program, which is hundreds times slower (see Table 1 in help for speed comparison). Accuracy can be further significantly improved by use of Fgenesh+ on Prot_Map output (see Table 2 in help fro accuracy comparison).