By Teresa M. Przytycka

This booklet constitutes the refereed lawsuits of the nineteenth Annual foreign convention on learn in Computational Molecular Biology, RECOMB 2015, held in Warsaw, Poland, in April 2015. The 36 prolonged abstracts have been conscientiously reviewed and chosen from one hundred seventy submissions. They file on unique examine in all parts of computational molecular biology and bioinformatics.

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Extra info for Research in Computational Molecular Biology: 19th Annual International Conference, RECOMB 2015, Warsaw, Poland, April 12-15, 2015, Proceedings

Example text

When the method of choice for generating candidate transformations sets is docking, the algorithm is limited to complexes which interaction graph has a star shaped spanning tree. In such cases, the resulted solution might not cover the whole complex. Therefore, top solutions of intermediate star shaped subcomplexes are integrated to produce a solution which covers the whole assembly. The integration is done by translating the top intermediate solutions to transformations sets and repeating the two last steps of the algorithm (Fig.

We follow the intuition that DASE in the transcriptome can be exploited to improve phasing power because SNP alleles within maternal and paternal haplotypes of a gene are present in the read data at (different) frequencies corresponding to the differential haplotypic expression (DHE). To solve this haplotype E. Berger and D. Yorukoglu—contributed equally. c Springer International Publishing Switzerland 2015 T. ): RECOMB 2015, LNBI 9029, pp. 28–29, 2015. 1007/978-3-319-16706-0 4 HapTree-X: An Integrative Bayesian Framework 29 reconstruction problem, we introduce a new maximum-likelihood formulation which takes into account DASE (generalizing that from HapTree [2]) and is thus able to newly exploit reads covering only one SNP.

In particular, for metagenomic data, there should be devised better ways to assess the appropriate value of the threshold for frequent k-mers. Apart from estimating it, an iterative process with decreasing values of thresholds may also be helpful. This can also be relevant for cases where reads have not been uniformly sampled across a genome. The overlap detection method should be made more robust to errors, even though this is not as problematic as it is for assemblers. The consensus derivation method could also be improved, especially in cases where repeats with different abundances are clustered together.

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