TAILIEUCHUNG - Báo cáo y học: " Ultrafast and memory-efficient alignment of short DNA sequences to the human genome"

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: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. | Open Access Software Ultrafast and memory-efficient alignment of short DNA sequences to the human genome Ben Langmead Cole Trapnell Mihai Pop and Steven L Salzberg Address Center for Bioinformatics and Computational Biology Institute for Advanced Computer Studies University of Maryland College Park MD 20742 USA. Correspondence Ben Langmead. Email langmead@ Published 4 March 2009 Genome Biology 2009 10 R25 doi gb-2009- 10-3-r25 The electronic version of this article is the complete one and can be found online at http 2009 10 3 R25 2009 Langmead et al. licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License http licenses by which permits unrestricted use distribution and reproduction in any medium provided the original work is properly cited. Received 21 October 2008 Revised 19 December 2008 Accepted 4 March 2009 Abstract Bowtie is an ultrafast memory-efficient alignment program for aligning short DNA sequence reads to large genomes. For the human genome Burrows-Wheeler indexing allows Bowtie to align more than 25 million reads per CPU hour with a memory footprint of approximately gigabytes. Bowtie extends previous Burrows-Wheeler techniques with a novel quality-aware backtracking algorithm that permits mismatches. Multiple processor cores can be used simultaneously to achieve even greater alignment speeds. Bowtie is open source http . Rationale Improvements in the efficiency of DNA sequencing have both broadened the applications for sequencing and dramatically increased the size of sequencing datasets. Technologies from Illumina San Diego CA USA and Applied Biosystems Foster City CA USA have been used to profile methylation patterns MeDIP-Seq 1 to map DNA-protein interactions ChIP-Seq 2 and to identify differentially expressed genes RNA-Seq 3 in the human genome and other species. The Illumina instrument was .

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