ExonHunter is a comprehensive gene finder based on hidden Markov models allowing use of variety of additional sources of information (ESTs, proteins, genome-genome comparison, repeats, and more).
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ExonHunter: a comprehensive approach to gene finding.
Brejová B, Brown DG, Li M, Vinar T.
Bioinformatics. 2005 Jun;21 Suppl 1:i57-65.