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Báo cáo y học: "The need for speed"

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: The need for speed. | Minireview The need for speed Paul Flicek Address European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK. Email flicek@ebi.ac.uk Published 27 March 2009 Genome Biology 2009 10 212 doi l0.ll86 gb-2009-l0-3-2l2 The electronic version of this article is the complete one and can be found online at http genomebiology.com 2009 l0 3 2l2 2009 BioMed Central Ltd Abstract DNA sequence data are being produced at an ever-increasing rate. The Bowtie sequence-alignment algorithm uses advanced data structures to help data analysis keep pace with data generation. In this month s Genome Biology Langmead and colleagues 1 present the Bowtie algorithm. Bowtie is designed to align large numbers of relatively short DNA sequencing reads to an entire reference genome. It does so by first taking the reference genome assembly and changing the order of the sequence using something called the Burrows-Wheeler Transform. Why is this useful Speed is the best answer Bowtie is more than 30 times faster than other published tools designed to do the same task. Let s step back and see why the need for speed in our analysis algorithms is greater now than at any time in the genomic age. Over the past three years massively high-throughput sequencing often called next-generation sequencing has developed from a few beta devices in key genome centers to a large installed base in research labs around the world. The success of sequencing machines such as Illumina Solexa ABI SOLiD and 454 FLX has facilitated the development of sequencing as a general-purpose experimental tool for many biological applications. The range of possible uses is rapidly establishing DNA sequencing as the microscope of modern biology. The scale of data generation is amazing for example in the course of its pilot phase the 1000 Genomes Project 2 has already generated almost 2 000-fold total coverage of the human genome from 180 individual samples an amount orders of magnitude larger than the .