Exonerate  is the successor to Genewise, a package of alignment tools for protein and EST to genome/DNA alignments with a splice-site aware algorithm. The output can parsed by Bio::SearchIO.
The details can be found in the references but there are several different models implemented in the tool. One model is est2genome which is effectively the same as EST2genome and Sim4. Another model is protein2genome which is a replacement for Genewise.
- Slater GS and Birney E. Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics. 2005 Feb 15;6:31. DOI:10.1186/1471-2105-6-31 |