Gene structure prediction V1.5

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EuGène[1] was trained based on our set of Physcomitrella patens reference genes, transcripts (ESTs and FLcDNAs) and homology evidences. While the resulting gene structures were quite promising, the prediction accuracy could still be improved combining all existing gene structure predictions and transcript alignments using EVidenceModeler[2]. The obtained gene structures, comprising only CDS exons, were updated using the PASA[3] alignment evidence to correct exon boundaries, adding UTRs and models for alternative splicing.

[1] EuGène: An Eucaryotic Gene Finder that combines several sources of evidence. T. Schiex, A. Moisan and P. Rouzé. Computational Biology, Eds. O. Gascuel and M-F. Sagot, LNCS 2066, pp. 111-125, 2001.

[2] Haas et al. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biology 2008, 9:R7doi:10.1186/gb-2008-9-1-r7.

[3] Haas, B.J., Delcher, A.L., Mount, S.M., Wortman, J.R., Smith Jr, R.K., Jr., Hannick, L.I., Maiti, R., Ronning, C.M., Rusch, D.B., Town, C.D. et al. (2003) Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res, 31, 5654-5666.

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