A comparative method for identification of gene structures and alternatively spliced variants

Bioinformatics
Trees-Juen ChuangMeng-Yuan Chou

Abstract

Alternative splicing (AS) serves as a mechanism to create diversity among functional proteins. Increasing evidence indicates that a large portion of genes have AS forms. Hence AS variants should be considered while analyzing gene structures. A new cross-species gene identification and AS analysis system, PSEP, has been developed. The system is based on expressed sequence tag (EST)-to-genome and genome-to-genome comparisons and is implemented in two steps: sequence alignment and a series of post-alignment processes, including progressive signal extraction and patching. For gene identification, these post-alignment processes serve as noise filters and enable PSEP to eliminate approximately 88% of potential overprediction. The overall accuracy of PSEP is better than or comparable to that of other well-known cross-species gene prediction programs, including the ROSETTA program, TWINSCAN, SGP-1/-2 and SLAM, when tested on three benchmark datasets (the ELN gene region, the HoxA cluster and the ROSETTA set). In addition, 76.2 and 76.0% of multiple-exon genes in the ROSETTA dataset and human chromosome 20, respectively, are found to have AS forms. Approximately 23% of the 210 elementary alternatives identified in the ROSETTA dataset ar...Continue Reading

Related Concepts

Related Feeds

Alternative splicing

Alternative splicing a regulated gene expression process that allows a single genetic sequence to code for multiple proteins. Here is that latest research.