Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts 英文参考文献.docVIP

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Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts 英文参考文献.doc

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Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts 英文参考文献

Open Access Research Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts Paul Flicek* and Michael R Brent? Addresses: *European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. ?Laboratory for Computational Genomics, Washington University, Saint Louis, MO 63130, USA. Correspondence: Paul Flicek. Email: flicek@ebi.ac.uk Published: 7 August 2006 Genome Biology 2006, 7(Suppl 1):S8 The electronic version of this article is the complete one and can be found online at /2006/7/S1/S8 ? 2006 Flicek and Brent; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: As part of the ENCODE Genome Annotation Assessment Project (EGASP), we developed the MARS extension to the Twinscan algorithm. MARS is designed to find human alternatively spliced transcripts that are conserved in only one or a limited number of extant species. MARS is able to use an arbitrary number of informant sequences and predicts a number of alternative transcripts at each gene locus. Results: MARS uses the mouse, rat, dog, opossum, chicken, and frog genome sequences as pair- wise informant sources for Twinscan and combines the resulting transcript predictions into genes based on coding (CDS) region overlap. Based on the EGASP assessment, MARS is one of the more accurate dual-genome prediction programs. Compared to the GENCODE annotation, we find that predictive sensitivity increases, while specificity decreases, as more informant species are used. MARS correctly predicts alternatively spliced transcripts for 11 of the 236 multi-exon GENCODE genes that are alternatively spliced in the coding region of the