A Polynomial Delay Algorithm for the Enumeration of Bubbles with Length Constraints in Directed Graphs and Its Application to the Detection of Alternative Splicing in RNA-seq Data

  • Gustavo Sacomoto
  • Vincent Lacroix
  • Marie-France Sagot
Conference paper

DOI: 10.1007/978-3-642-40453-5_9

Part of the Lecture Notes in Computer Science book series (LNCS, volume 8126)
Cite this paper as:
Sacomoto G., Lacroix V., Sagot MF. (2013) A Polynomial Delay Algorithm for the Enumeration of Bubbles with Length Constraints in Directed Graphs and Its Application to the Detection of Alternative Splicing in RNA-seq Data. In: Darling A., Stoye J. (eds) Algorithms in Bioinformatics. WABI 2013. Lecture Notes in Computer Science, vol 8126. Springer, Berlin, Heidelberg

Abstract

We present a new algorithm for enumerating bubbles with length constraints in directed graphs. This problem arises in transcriptomics, where the question is to identify all alternative splicing events present in a sample of mRNAs sequenced by RNA-seq. This is the first polynomial-delay algorithm for this problem and we show that in practice, it is faster than previous approaches. This enables us to deal with larger instances and therefore to discover novel alternative splicing events, especially long ones, that were previously overseen using existing methods.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Gustavo Sacomoto
    • 1
    • 2
    • 3
  • Vincent Lacroix
    • 1
    • 2
    • 3
  • Marie-France Sagot
    • 1
    • 2
    • 3
  1. 1.INRIA Rhône-AlpesMontbonnot Saint-MartinFrance
  2. 2.Université de LyonLyonFrance
  3. 3.CNRS, UMR5558, Laboratoire de Biométrie et Biologie ÉvolutiveUniversité Lyon 1VilleurbanneFrance

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