Genewise

Ewan Birney's PhD thesis thesis 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 thesis 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

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1. thesis Birney E, Cambridge University, PhD Thesis.
2. birney00 pmid=10779496
3. birney01 Birney E. "Hidden Markov Models in Biological Sequence Analysis" IBM J Res and Dev 2001; 45(3/4): 449-454.
4. birney04 pmid=15123596

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