Publication details

Jakub Kovac, Tomas Vinar, Brona Brejova. Predicting Gene Structures from Multiple RT-PCR Tests. In S.L. Salzberg, T. Warnow, ed., Workshop on Algorithms in Bioinformatics (WABI 2009), 5724 volume of Lecture Notes in Bioinformatics, pp. 181-193, Philadelphia, PA, USA, September 2009. Springer.
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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. We 
also apply our methods to a real RT-PCR data set in the Drosophila genome. 
We conclude that the use of RT-PCR data sets can improve the sensitivity of
gene prediction and locate novel splicing variants.



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