Abstract
BackgroundAs 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.ResultsMARS uses the mouse, rat, dog, opossum, chicken, and frog genome sequences as pairwise 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 their transcripts. For these genes a total of 24 correct transcripts are predicted.ConclusionThe MARS algorithm is able to predict alternatively spliced transcripts without the use of expressed sequence information, although the number of loci in which multiple predicted transcripts match multiple alternatively spliced transcripts in the GENCODE annotation is relatively small.
Highlights
As part of the ENCODE Genome Annotation Assessment Project (EGASP), we developed the MARS extension to the Twinscan algorithm
The results for the updated MARS algorithm differ from those reported in the EGASP summary because of the updates to the MARS algorithm that are described above
Compared to the submitted predictions, those produced from the updated MARS algorithm are more sensitive compared to the GENCODE annotation, but less specific at both the transcript and exon levels
Summary
As part of the ENCODE Genome Annotation Assessment Project (EGASP), we developed the MARS extension to the Twinscan algorithm. MARS is able to use an arbitrary number of informant sequences and predicts a number of alternative transcripts at each gene locus. In the past decade the most important advance in de novo gene prediction came with the initial availability of extensive human and mouse genomic sequences. Dualgenome gene prediction algorithms most often use the mouse genome sequence as a source of evolutionary conservation information. This was originally a consequence of the early availability, with respect to other mammals, of the mouse genome sequence [5,6,7,8]. As additional genomes were sequenced, it became apparent that the
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