Summary: The MSAViewer is a quick and easy visualization and analysis JavaScript component for Multiple Sequence Alignment data of any size. Core features include interactive navigation through the alignment, application of popular color schemes, sorting, selecting and filtering. The MSAViewer is ‘web ready’: written entirely in JavaScript, compatible with modern web browsers and does not require any specialized software. The MSAViewer is part of the BioJS collection of components.Availability and Implementation: The MSAViewer is released as open source software under the Boost Software License 1.0. Documentation, source code and the viewer are available at http://msa.biojs.net/.Supplementary information:
Supplementary data are available at Bioinformatics online.Contact:
msa@bio.sh
BioJS is an open source software project that develops visualization tools for different types of biological data. Here we report on the factors that influenced the growth of the BioJS user and developer community, and outline our strategy for building on this growth. The lessons we have learned on BioJS may also be relevant to other open source software projects.DOI:
http://dx.doi.org/10.7554/eLife.07009.001
In the classical interval scheduling type of problems, a set of n jobs, characterized by their start and end time, need to be executed by a set of machines, under various constraints. In this paper we study a new variant in which the jobs need to be assigned to at most k identical machines, such that the minimum number of machines that are busy at the same time is maximized. This is relevant in the context of genome sequencing and haplotyping, specifically when a set of DNA reads aligned to a genome needs to be pruned so that no more than k reads overlap, while maintaining as much read coverage as possible across the entire genome. We show that the problem can be solved in time min O(n 2 log k/ log n), O(nk log k) by using max-flows. We also give an O(n log n)-time approximation algorithm with approximation ratio ρ = k k/2 .
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