A method for detecting short initial exons

There are many gene prediction programs available and while the accuracy of these programs has increased significantly over the last few years, the accurate identification of short exons remains very poor. In this paper we concentrate on short initial exons and present a method to improve the detection of these short coding regions. The algorithm is based on the weight array method (WAM) and CpG islands. The algorithm was evaluated on a total of 158 sequences containing short initial exons, and achieves an accuracy of up to 73%. By comparison with GENSCAN, the proposed WAM-CpG Island algorithm reveals an improvement of up to 22%.