A method of consolidating and combining EST and mRNA alignments to a genome to enumerate supported splice variants

Abstract

Many researchers have focused their attention on alternative splice forms of genes as a means to explain the apparent complexity of human and other higher eukaryotic organisms. The exonintron structure implied by aligning ESTs and mRNAs to genomic sequence provides a useful basis for comparing different splice forms. There are software tools that enumerate all possible exonintron combinations implied by these alignments, but this approach has potential drawbacks including a combinatorial explosion in the number of splice forms and the generation of many unsupported splice forms. Alt Merge retains information about exon combinations present in the input alignments. It uses this information to combine compatible subsets of the alignments into a single representative form. Substructures of these representative forms are then exchanged to enumerate only those alternative splice forms that are consistent with the input alignments.