Predicting Gene Structures from Multiple RT-PCR Tests

(Extended Abstract)
  • Jakub Kováč
  • Tomáš Vinař
  • Broňa Brejová
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5724)

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.

Keywords

gene finding RT-PCR NP-completeness dynamic programming splicing graph 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  • Jakub Kováč
    • 1
  • Tomáš Vinař
    • 2
  • Broňa Brejová
    • 1
  1. 1.Department of Computer ScienceComenius UniversityBratislavaSlovakia
  2. 2.Department of Applied InformaticsComenius UniversityBratislavaSlovakia

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