A method for detecting short initial exons

Author

Logeswaran, Sayanthan ; Ambikairajah, Eliathamby ; Epps, Julien

Author_Institution

Sch. of Electr. Eng. & Telecommun., Univ. of New South Wales, Sydney, NSW

fYear

2006

fDate

28-30 May 2006

Firstpage

61

Lastpage

62

Abstract

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%.

Keywords

biology computing; genetics; CpG island algorithm; GENSCAN; WAM; gene prediction programs; short coding regions; short initial exons detection; weight array method; Australia; Bioinformatics; DNA; Genomics; Length measurement; Packaging; Predictive models; Proteins; Sequences; Statistics;

fLanguage

English

Publisher

ieee

Conference_Titel

Genomic Signal Processing and Statistics, 2006. GENSIPS '06. IEEE International Workshop on

Conference_Location

College Station, TX

Print_ISBN

1-4244-0384-7

Electronic_ISBN

1-4244-0385-5

Type

conf

DOI

10.1109/GENSIPS.2006.353156

Filename

4161777