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Genome threader 

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GenomeThreader is a software tool to compute gene structure predictions. The gene structure predictions are calculated using a similarity-based approach where additional cDNA/EST and/or protein sequences are used to predict gene structures via spliced alignments. The intron cutout technique allows to overcome the time and space limitations of the dynamic programming (DP) algorithms, in particular, when applied to organisms containing long introns. With BSSMs (Baysian Splice Site Models) it is possible to assign probabilities to GT donor, GC donor, and AG acceptor sites. This information is used in the DP to get the exact exon/intron boundaries right. Combination of cDNA/EST Based Spliced Alignments with Protein Based Spliced Alignments: After (spliced) aligning the supplied cDNAs/ESTs and protein sequences onto the genomic template, GenomeThreader computes consensus spliced alignments. Consensus spliced alignments combine several spliced alignments to resolve the complete gene structure and to uncover alternative splicing. (http://www.genomethreader.org/ )