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Open Access Method

A computational investigation of kinetoplastid trans-splicing

Shuba Gopal12*, Saria Awadalla1, Terry Gaasterland2 and George AM Cross3

Author Affiliations

1 Laboratory of Computational Genomics, Rockefeller University, 1230 York Avenue, New York, NY 10021, USA

2 Department of Biological Sciences, Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623, USA

3 Laboratory of Molecular Parasitology, Rockefeller University, 1230 York Avenue, New York, NY 10021, USA

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Genome Biology 2005, 6:R95  doi:10.1186/gb-2005-6-11-r95

Published: 17 October 2005

Abstract

Trans-splicing is an unusual process in which two separate RNA strands are spliced together to yield a mature mRNA. We present a novel computational approach which has an overall accuracy of 82% and can predict 92% of known trans-splicing sites. We have applied our method to chromosomes 1 and 3 of Leishmania major, with high-confidence predictions for 85% and 88% of annotated genes respectively. We suggest some extensions of our method to other systems.