The Twinscan program predicts genes in a manner similar to Genscan, except that Twinscan takes advantage of genome comparison to improve gene prediction accuracy. More information and a web server can be found at http://genes.cs.wustl.edu/.
The Twinscan algorithm is described in Korf I, Flicek P, Duan D, and Brent MR (2001), "Integrating genomic homology into gene structure prediction", Bioinformatics 17:S140-148.
Thanks to Michael Brent's Computational Genomics Group at Washington University St. Louis for providing these data.