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VarDetect: a nucleotide sequence variation exploratory tool

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13 pages
Single nucleotide polymorphisms (SNPs) are the most commonly studied units of genetic variation. The discovery of such variation may help to identify causative gene mutations in monogenic diseases and SNPs associated with predisposing genes in complex diseases. Accurate detection of SNPs requires software that can correctly interpret chromatogram signals to nucleotides. Results We present VarDetect, a stand-alone nucleotide variation exploratory tool that automatically detects nucleotide variation from fluorescence based chromatogram traces. Accurate SNP base-calling is achieved using pre-calculated peak content ratios, and is enhanced by rules which account for common sequence reading artifacts. The proposed software tool is benchmarked against four other well-known SNP discovery software tools (PolyPhred, novoSNP, Genalys and Mutation Surveyor) using fluorescence based chromatograms from 15 human genes. These chromatograms were obtained from sequencing 16 two-pooled DNA samples; a total of 32 individual DNA samples. In this comparison of automatic SNP detection tools, VarDetect achieved the highest detection efficiency. Availability VarDetect is compatible with most major operating systems such as Microsoft Windows, Linux, and Mac OSX. The current version of VarDetect is freely available at http://www.biotec.or.th/GI/tools/vardetect .
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BMC Bioinformatics
BioMedCentral
Open Access Research VarDetect: a nucleotide sequence variation exploratory tool 1 2 Chumpol Ngamphiw, Supasak Kulawonganunchai, 3 11 Anunchai Assawamakin, Ekachai Jenwitheesukand Sissades Tongsima*
1 Address: GenomeInstitute, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phaholyothin Road, Klong 2 1, Klong Luang, Pathumthani 12120, Thailand,Department of Computer Science, School of Engineering and Technology, Asian Institute of 3 Technology, P.O. Box 4, Klong Luang, Pathumthani 12120, Thailand andDivision of Medical Genetics, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand Email: Chumpol Ngamphiw  chumpol.nga@biotec.or.th; Supasak Kulawonganunchai  ksupasak@gmail.com; Anunchai Assawamakin  anunchai_ice@yahoo.com; Ekachai Jenwitheesuk  ekachai@biotec.or.th; Sissades Tongsima*  sissades@biotec.or.th * Corresponding author
fromAsia Pacific Bioinformatics Network (APBioNet) Seventh International Conference on Bioinformatics (InCoB2008) Taipei, Taiwan. 20–23 October 2008
Published: 12 December 2008 BMC Bioinformatics2008,9(Suppl 12):S9
doi:10.1186/1471-2105-9-S12-S9
<supplement> <title> <p>Seventh International Conference on Bioinformatics (InCoB2008)</p> </title> <editor>Shoba Ranganathan, Wen-Lian Hsu, Ueng-Cheng Yang and Tin Wee Tan</editor> <note>Proceedings</note> </supplement> This article is available from: http://www.biomedcentral.com/1471-2105/9/S12/S9 © 2008 Ngamphiw 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 Background:Single nucleotide polymorphisms (SNPs) are the most commonly studied units of genetic variation. The discovery of such variation may help to identify causative gene mutations in monogenic diseases and SNPs associated with predisposing genes in complex diseases. Accurate detection of SNPs requires software that can correctly interpret chromatogram signals to nucleotides. Results:We present VarDetect, a stand-alone nucleotide variation exploratory tool that automatically detects nucleotide variation from fluorescence based chromatogram traces. Accurate SNP base-calling is achieved using pre-calculated peak content ratios, and is enhanced by rules which account for common sequence reading artifacts. The proposed software tool is benchmarked against four other well-known SNP discovery software tools (PolyPhred, novoSNP, Genalys and Mutation Surveyor) using fluorescence based chromatograms from 15 human genes. These chromatograms were obtained from sequencing 16 two-pooled DNA samples; a total of 32 individual DNA samples. In this comparison of automatic SNP detection tools, VarDetect achieved the highest detection efficiency. Availability:VarDetect is compatible with most major operating systems such as Microsoft Windows, Linux, and Mac OSX. The current version of VarDetect is freely available at http:// www.biotec.or.th/GI/tools/vardetect.
Background Following completion of the human genome project, detection and discovery of single nucleotide polymor
phisms (SNPs) is at the forefront of genomic research. The discovery of SNPs may help to identify causative gene mutations in monogenic diseases as well as SNPs associ
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