Download Bioinformatics Research and Applications: 12th International by Anu Bourgeois, Pavel Skums, Xiang Wan, Alex Zelikovsky PDF

By Anu Bourgeois, Pavel Skums, Xiang Wan, Alex Zelikovsky

ISBN-10: 3319387812

ISBN-13: 9783319387819

ISBN-10: 3319387820

ISBN-13: 9783319387826

This e-book constitutes the lawsuits of the twelfth overseas Symposium on Bioinformatics learn and functions, ISBRA 2016, held in Minsk, Belarus, in June 2016.
The 25 papers awarded during this quantity have been rigorously reviewed and chosen from seventy seven submissions. They have been equipped in topical sections named: subsequent iteration sequencing facts research; protein-protein interactions and networks; protein and RNA constitution; phylogenetics; series research; and statistical methods.

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Additional resources for Bioinformatics Research and Applications: 12th International Symposium, ISBRA 2016, Minsk, Belarus, June 5-8, 2016, Proceedings

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C. ) ASIAN 1996. LNCS, vol. 1179, pp. 11–22. Springer, Heidelberg (1996) 23. : Efficient construction of an assembly string graph using the FM-index. Bioinformatics 26(12), i367–i373 (2010) 24. : Efficient de novo assembly of large genomes using compressed data structures. Genome Res. 22, 549–556 (2012) 25. : ABySS: a parallel assembler for short read sequence data. Genome Res. jp Abstract. Detection of somatic mutations from tumor and matched normal sequencing data has become a standard approach in cancer research.

For example, reads obtained by Illumina technology (which is the most used) have length between 50 and 150 bases [21]. To analyze datasets coming from different technologies, hence with a large variation of read lengths, an approach based on same-length strings is likely to be limiting, as witnessed by the recent introduction of variable-length de Bruijn graphs [9]. The string graph [18] representation is an alternative approach that does not need to break the reads into k-mers (as in the de Bruijn graphs), and has the advantage of immediately distinguishing the repeats that result in different arcs.

Another string graph assembler is Fermi [17] which implements a variant of the original SGA algorithm [23] that is tailored for SNP and variant calling. A number of recent works face the problem of designing efficient algorithmic strategies or data structures for building string graphs. Among those works we can find a string graph assembler [4], based on a careful use of hashing and Bloom filters, with performance comparable with the first SGA implementation [23]. Another important alternative approach to SGA is Readjoiner [15] which is based on an efficient computation of a subset of exact suffix-prefix matches, and by subsequent rounds of suffix sorting, scanning, and filtering outputs the non-redundant arcs of the graph.

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Bioinformatics Research and Applications: 12th International Symposium, ISBRA 2016, Minsk, Belarus, June 5-8, 2016, Proceedings by Anu Bourgeois, Pavel Skums, Xiang Wan, Alex Zelikovsky


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