TWAIN is a software to predict genes simultaneously in two closely related eukaryotic organisms.TWAIN is a new syntenic genefinder which employs a Generalized Pair Hidden Markov Model (GPHMM) to predict genes in two closely related eukaryotic genomes simultaneously.It utilizes the MUMmer package to perform approximate alignment before applying a GPHMM based on an enhanced version of the TigrScan gene finder.
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Majoros W.H., Pertea M., Salzberg S.L. (2005) Efficient implementation of a Generalized Pair Hidden Markov Model for comparative gene finding. Bioinformatics 21 1782-1788.