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Báo cáo y học: "Tools for simulating evolution of aligned genomic regions with integrated parameter estimation"

Tuyển tập các báo cáo nghiên cứu về y học được đăng trên tạp chí y học Minireview cung cấp cho các bạn kiến thức về ngành y đề tài: Tools for simulating evolution of aligned genomic regions with integrated parameter estimation. | Open Access Software Tools for simulating evolution of aligned genomic regions with integrated parameter estimation Avinash Varadarajan Robert KBradley and Ian H Holmes Addresses Computer Science Division University of California Berkeley CA 94720-1776 USA. Biophysics Graduate Group University of California Berkeley CA 94720-3200 USA. Department of Bioengineering University of California Berkeley CA 94720-1762 USA. Correspondence Ian H Holmes. Email ihh@berkeley.edu Published 8 October 2008 Genome Biology 2008 9 RI47 doi I0.II86 gb-2008-9- I0-r 147 The electronic version of this article is the complete one and can be found online at http genomebiology.com 2008 9 I0 RI47 Received 20 June 2008 Revised 21 August 2008 Accepted 8 October 2008 2008 Varadarajan et al. licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License http creativecommons.org licenses by 2.0 which permits unrestricted use distribution and reproduction in any medium provided the original work is properly cited. Abstract Controlled simulations of genome evolution are useful for benchmarking tools. However many simulators lack extensibility and cannot measure parameters directly from data. These issues are addressed by three new open-source programs GSIMULATOR for neutrally evolving DNA SIMGRAM for generic structured features and SIMGENOME for syntenic genome blocks . Each offers algorithms for parameter measurement and reconstruction of ancestral sequence. All three tools out-perform the leading neutral DNA simulator DAWG in benchmarks. The programs are available at http biowiki.org SimulationTools. Rationale Almost every kind of genome annotation tool has at some point in its lifecycle been benchmarked on simulated data. Exceptions occur when the data are too poorly understood to be simulated or so well understood that simulation is unnecessary. For the regime in between generation of synthetic datasets is a nontrivial task. .