Recognizing translation initiation sites of eukaryotic genes based on the cooperatively scanning model

MOTIVATION: Translation initiation sites (TISs) of genes are the key points of protein synthesis. Exact recognition of TISs in eukaryotic genes is one of the most important tasks in gene-finding algorithms. However, the task has not been satisfactorily fulfilled up to the present. Here, we propose a cooperatively scanning model for recognizing TISs and the first exons of eukaryotic genes on the basis of the structural characteristics of multi-exon genes. RESULTS: The model was employed to cooperatively scan the TISs and 3' splicing sites in eukaryotic genes, and the TISs and the first exons of 132 mammalian gene sequences are identified to evaluate the model. Accuracy of exactly recognizing the TISs and the first exons has been found to amount respectively to 64.4 and 51.5%. We believe that the model will be a useful tool for genome annotation and that it can be easily incorporated into other algorithms to achieve higher accuracy in recognizing TISs and the first exons. AVAILABILITY: The program is available upon request.