Computational analysis of alternative spliced genes on maize chromosome 1

Alternative splicing is an important part of mRNA processing which results in protein diversity in all eukaryotes. In plants, this process is still poorly understood, however recent computational analysis has shown that alternative splicing is far more prevalent than previously thought. For better characterization of alternative splicing in maize, one of the most important crop species, we used AUGUSTUS (web-application deployed on local or remote host) to predict multiple transcripts and alternative splicing events from maize chromosome 1 sequence. From over 300 million bp of chromosome 1, AUGUSTUS software predicted ab initio 46 400 genes and 20% of the estimated genes have at least two transcripts. For 412 genes with three transcripts we performed additional analysis including EST's alignment, protein identification and comparative evaluation with genes predicted using F genesh and Gramene software. In consequence we have identified alternative splicing events for 42 genes from maize chromosome 1.