Genomewise

Part of Ewan Birney's Wise package, Genomewise incorporates EST (no reading frame) and protein alignment information (reading frame) with a genomic sequence to predict a set of ORFs on a contig. You should have already aligned the ESTs and proteins to the genomic region and this tool is aggregating that information into a single set of gene predictions.

exon 120 340
exon 560 591
//
cds  12  56 0
cds  70  80 1

See also Genewise for more information on obtaining the package.