Genewise

From BioPerl

Ewan Birney's PhD thesis [1] was in a large part the development of the Wise system for building a system to generate C code for sequence alignment algorithms based on a simple language describing the algorithm. The Dynamite compiler [1] is used to convert the dynamic programming representation into compilable C code.

Genewise is available from this EBI site. One should also look at the newer version which is not officially released but has additional functionality like pseudogene prediction.

References

1. Birney E, Cambridge University, PhD Thesis. [thesis]
2. Birney E and Durbin R. Using GeneWise in the Drosophila annotation experiment. Genome Res 2000 Apr; 10(4) 547-8. pmid:10779496. PubMed HubMed [birney00]
3. Birney E. "Hidden Markov Models in Biological Sequence Analysis" IBM J Res and Dev 2001; 45(3/4): 449-454.

   [birney01]

4. Birney E, Clamp M, and Durbin R. GeneWise and Genomewise. Genome Res 2004 May; 14(5) 988-95. doi:10.1101/gr.1865504 pmid:15123596. PubMed HubMed [birney04]

All Medline abstracts: PubMed HubMed