Abstract
Polymorphisms in DNA- or RNA-seq data lead to recognisable patterns in a de Bruijn graph representation of the reads obtained by sequencing. Such patterns have been called mouths, or bubbles in the literature. They correspond to two vertex-disjoint directed paths between a source s and a target t. Due to the high number of such bubbles that may be present in real data, their enumeration is a major issue concerning the efficiency of dedicated algorithms. We propose in this paper the first linear delay algorithm to enumerate all bubbles with a given source.
This work was supported by the french ANR MIRI BLAN08-1335497 Project and the ERC Advanced Grant Sisyphe held by Marie-France Sagot. Partially supported by Italian project PRIN AlgoDEEP (2008TFBWL4) of MIUR. The second author received additional support from the Italian PRIN project ’DISCO’.
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References
Robertson, G., et al.: De novo assembly and analysis of RNA-seq data. Nature Methods 7(11), 909–912 (2010)
Sacomoto, G., et al.: KisSplice: de-novo calling alternative splicing events from rna-seq data. In: RECOMB-Seq, BMC Bioinformatics (2012)
Simpson, J.T., et al.: ABySS: A parallel assembler for short read sequence data. Genome Research 19(6), 1117–1123 (2009)
Peterlongo, P., Schnel, N., Pisanti, N., Sagot, M.-F., Lacroix, V.: Identifying SNPs without a Reference Genome by Comparing Raw Reads. In: Chavez, E., Lonardi, S. (eds.) SPIRE 2010. LNCS, vol. 6393, pp. 147–158. Springer, Heidelberg (2010)
Gusfield, D., Eddhu, S., Langley, C.H.: Optimal, efficient reconstruction of phylogenetic networks with constrained recombination. J. Bioinf. and Comput. Biol. 2(1), 173–214 (2004)
Iqbal, Z., Caccamo, M., Turner, I., Flicek, P., McVean, G.: De novo assembly and genotyping of variants using colored de bruijn graphs. Nature Genetics (2012)
Johnson, D.B.: Finding all the elementary circuits of a directed graph. SIAM J. Comput. 4(1), 77–84 (1975)
Pevzner, P.A., Tang, H., Tesler, G.: De novo repeat classification and fragment assembly. In: RECOMB, pp. 213–222 (2004)
Sammeth, M.: Complete alternative splicing events are bubbles in splicing graphs. J. Comput. Biol. 16(8), 1117–1140 (2009)
Tarjan, R.E.: Enumeration of the elementary circuits of a directed graph. SIAM Journal on Computing 2(3), 211–216 (1973)
Tiernan, J.C.: An efficient search algorithm to find the elementary circuits of a graph. Commun. ACM 13(12), 722–726 (1970)
Zerbino, D.R., Birney, E.: Velvet: Algorithms for de novo short read assembly using de bruijn graphs. Genome Research 18(5), 821–829 (2008)
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Birmelé, E. et al. (2012). Efficient Bubble Enumeration in Directed Graphs. In: Calderón-Benavides, L., González-Caro, C., Chávez, E., Ziviani, N. (eds) String Processing and Information Retrieval. SPIRE 2012. Lecture Notes in Computer Science, vol 7608. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-34109-0_13
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DOI: https://doi.org/10.1007/978-3-642-34109-0_13
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