AGenDA is a gene-prediction tool that is based on cross-species sequence comparison. The software tools CHAOS and DIALIGN are used to align a pair of syntenic genomic sequences, e.g. from human and mouse. AGenDA searches for conserved splice sites and start/stop codons at the boundaries of identified sequence homologies in order to identify potential exons.
GeneAlign is a gene prediction tool that uses conservation of gene structures and sequence homologies between protein coding regions to increase prediction accuracy. GeneAlign is currently configured to align human and mouse sequences for gene prediction.
NCBI. The ORF Finder (Open Reading Frame Finder) is a graphical analysis tool which finds all open reading frames of a selectable minimum size in a user's sequence or in a sequence already in the database.