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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References
KisSplice’s manual (2013), http://kissplice.prabi.fr/documentation
Ahuja, R.K., Mehlhorn, K., Orlin, J.B., Tarjan, R.E.: Faster algorithms for the Shortest Path Problem. J. ACM 37, 213–223 (1990)
Birmelé, E., Crescenzi, P., Ferreira, R.A., Grossi, R., Lacroix, V., Marino, A., Pisanti, N., Sacomoto, G.A.T., Sagot, M.-F.: Efficient bubble enumeration in directed graphs. In: Calderón-Benavides, L., González-Caro, C., Chávez, E., Ziviani, N. (eds.) SPIRE 2012. LNCS, vol. 7608, pp. 118–129. Springer, Heidelberg (2012)
Chen, M., Chowdhury, R.A., Ramachandran, V., Roche, D.L., Tong, L.: Priority Queues and Dijkstra’s Algorithm. Technical Report TR-07-54 (2007)
Chikhi, R., Rizk, G.: Space-efficient and exact de bruijn graph representation based on a bloom filter. In: Raphael, B., Tang, J. (eds.) WABI 2012. LNCS, vol. 7534, pp. 236–248. Springer, Heidelberg (2012)
Cormen, T.H., Stein, C., Rivest, R.L., Leiserson, C.E.: Introduction to Algorithms, 2nd edn. McGraw-Hill Higher Education (2001)
Grabherr, M.G., Haas, B.J., Yassour, M., Levin, J.Z., Thompson, D.A., et al.: Full-length transcriptome assembly from RNA-seq data without a reference genome. Nat. Biotechnol. 29, 644–652 (2011)
Iqbal, Z., Caccamo, M., Turner, I., Flicek, P., McVean, G.: De novo assembly and genotyping of variants using colored de Bruijn graphs. Nat. Genetics (2012)
Li, C.-L., McCormick, S.T., Simchi-Levi, D.: The complexity of finding two disjoint paths with min-max objective function. Disc. Appl. Math. (1990)
Mortazavi, A., Williams, B., McCue, K., Schaeffer, L., Wold, B.: Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5, 621–628 (2008)
Pruitt, K., Tatusova, T., Klimke, W., Maglott, D.: NCBI reference sequences: current status, policy and new initiatives. Nucleic Acids Research 37(Database-Issue), 32–36 (2009)
Robertson, G., Schein, J., Chiu, R., Corbett, R., et al.: De novo assembly and analysis of RNA-seq data. Nat. Methods 7, 909–912 (2010)
Sacomoto, G.A.T., Kielbassa, J., Chikhi, R., Uricaru, R., Antoniou, P., Sagot, M.-F., Peterlongo, P., Lacroix, V.: Kissplice: de-novo calling alternative splicing events from RNA-seq data. BMC Bioinformatics 13, S5 (2012)
Schulz, M.H., Zerbino, D.R., Vingron, M., Birney, E.: Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics 28, 1086–1092 (2012)
Wang, E., Sandberg, R., Luo, S., Khrebtukova, I., Zhang, L., Mayr, C., Kingsmore, S., Schroth, G.P., Burge, C.: Alternative isoform regulation in human tissue transcriptomes. Nature 456(7221), 470–476 (2008)
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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
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