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Studies from Beijing Genomics Institute in the area of life sciences described
2009 AUG 3 - (NewsRx.com) -- Investigators publish new data in the report 'SOAP2: an improved ultrafast tool for short read alignment.' According to a study from Shenzhen, People's Republic of China, "SOAP2 is a significantly improved version of the short oligonucleotide alignment program that both reduces computer memory usage and increases alignment speed at an unprecedented rate. We used a Burrows Wheeler Transformation (BWT) compression index to substitute the seed strategy for indexing the reference sequence in the main memory." The researchers concluded: "SOAP2 is a significantly improved version of the short oligonucleotide alignment program that both reduces computer memory usage and increases alignment speed at an unprecedented rate. We used a Burrows Wheeler Transformation (BWT) compression index to substitute the seed strategy for indexing the reference sequence in the main memory. We tested it on the whole human genome and found that this new algorithm reduced memory usage from 14.7 to 5.4 GB and improved alignment speed by 20-30 times. SOAP2 is compatible with both single-and paired-end reads. Additionally, this tool now supports multiple text and compressed file formats. A consensus builder has also been developed for consensus assembly and SNP detection from alignment of short reads on a reference genome. AVAILABILITY: http://soap.genomics.org.cn." Li and colleagues published their study in Bioinformatics (SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics, 2009;25(15):1966-7). For more information, contact R. Li, Beijing Genomics Institute at Shenzhen, Shenzhen, 518083, China. Publisher contact information for the journal Bioinformatics is: Oxford University Press, Great Clarendon St., Oxford OX2 6DP, England. Keywords: People's Republic of China, Shenzhen, Life Sciences, BioInformatics LLC, Biotechnology Business, Biotechnology Company. This article was prepared by Biotech Business Week editors from staff and other reports. Copyright 2009, Biotech Business Week via NewsRx.com.
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