Predicting gene structures from multiple RT-PCR tests

Authors:
Jakub Kováč;Tomáš Vinař;Broňa Brejová
Affiliations:
Department of Computer Science, Comenius University, Bratislava, Slovakia;Department of Applied Informatics, Comenius University, Bratislava, Slovakia;Department of Computer Science, Comenius University, Bratislava, Slovakia
Venue:
WABI'09 Proceedings of the 9th international conference on Algorithms in bioinformatics
Year:
2009

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Abstract

It has been demonstrated that the use of additional information such as ESTs and protein homology can significantly improve accuracy of gene prediction. However, many sources of external information are still being omitted from consideration. Here, we investigate the use of product lengths from RT-PCR experiments in gene finding. We present hardness results and practical algorithms for several variants of the problem and apply our methods to a real RT-PCR data set in the Drosophila genome. We conclude that the use of RT-PCR data can improve the sensitivity of gene prediction and locate novel splicing variants.