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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

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Part of the Lecture Notes in Computer Science book series (LNBI,volume 8126)

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.

Keywords

  • Priority Queue
  • Alternative Splice Event
  • Length Constraint
  • Next Generation Sequencing Data
  • Short Path Tree

These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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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. https://doi.org/10.1007/978-3-642-40453-5_9

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  • DOI: https://doi.org/10.1007/978-3-642-40453-5_9

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-40452-8

  • Online ISBN: 978-3-642-40453-5

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