SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation.

@article{citeulike:1654327, abstract = {MOTIVATION: Single nucleotide polymorphisms (SNPs) analysis is an important means to study genetic variation. A fast and cost-efficient approach to identify large numbers of novel candidates is the SNP mining of large scale sequencing projects. The increasing availability of sequence trace data in public repositories makes it feasible to evaluate SNP predictions on the DNA chromatogram level. MAVIANT, a platform-independent Multipurpose Alignment VIewing and Annotation Tool, provides DNA chromatogram and alignment views and facilitates evaluation of predictions. In addition, it supports direct manual annotation, which is immediately accessible and can be easily shared with external collaborators. RESULTS: Large-scale SNP mining of polymorphisms bases on porcine EST sequences yielded more than 7900 candidate SNPs in coding regions (cSNPs), which were annotated relative to the human genome. Non-synonymous SNPs were analyzed for their potential effect on the protein structure/function using the PolyPhen and SIFT prediction programs. Predicted SNPs and annotations are stored in a web-based database. Using MAVIANT SNPs can visually be verified based on the DNA sequencing traces. A subset of candidate SNPs was selected for experimental validation by resequencing and genotyping. This study provides a web-based DNA chromatogram and contig browser that facilitates the evaluation and selection of candidate SNPs, which can be applied as genetic markers for genome wide genetic studies. AVAILABILITY: The stand-alone version of MAVIANT program for local use is freely available under GPL license terms at http://snp.agrsci.dk/maviant. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, address = {Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, University of Aarhus, DK-8830 Tjele, Denmark.}, author = {Panitz, F. and Stengaard, H. and Hornshøj, H. and Gorodkin, J. and Hedegaard, J. and Cirera, S. and Thomsen, B. and Madsen, L. B. and Høj, A. and Vingborg, R. K. and Zahn, B. and Wang, X. and Wang, X. and Wernersson, R. and Jørgensen, C. B. and Scheibye-Knudsen, K. and Arvin, T. and Lumholdt, S. and Sawera, M. and Green, T. and Nielsen, B. J. and Havgaard, J. H. and Brunak, S. and Fredholm, M. and Bendixen, C. }, citeulike-article-id = {1654327}, issn = {1460-2059}, journal = {Bioinformatics}, month = {July}, number = {13}, posted-at = {2007-09-14 05:08:44}, priority = {2}, title = {SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation.}, url = {http://view.ncbi.nlm.nih.gov/pubmed/17646321}, volume = {23}, year = {2007} }

TY - JOUR ID - citeulike:1654327 L3 - citeulike-article-id:1654327 TI - SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation. JF - Bioinformatics VL - 23 IS - 13 AD - Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, University of Aarhus, DK-8830 Tjele, Denmark. SN - 1460-2059 N2 - MOTIVATION: Single nucleotide polymorphisms (SNPs) analysis is an important means to study genetic variation. A fast and cost-efficient approach to identify large numbers of novel candidates is the SNP mining of large scale sequencing projects. The increasing availability of sequence trace data in public repositories makes it feasible to evaluate SNP predictions on the DNA chromatogram level. MAVIANT, a platform-independent Multipurpose Alignment VIewing and Annotation Tool, provides DNA chromatogram and alignment views and facilitates evaluation of predictions. In addition, it supports direct manual annotation, which is immediately accessible and can be easily shared with external collaborators. RESULTS: Large-scale SNP mining of polymorphisms bases on porcine EST sequences yielded more than 7900 candidate SNPs in coding regions (cSNPs), which were annotated relative to the human genome. Non-synonymous SNPs were analyzed for their potential effect on the protein structure/function using the PolyPhen and SIFT prediction programs. Predicted SNPs and annotations are stored in a web-based database. Using MAVIANT SNPs can visually be verified based on the DNA sequencing traces. A subset of candidate SNPs was selected for experimental validation by resequencing and genotyping. This study provides a web-based DNA chromatogram and contig browser that facilitates the evaluation and selection of candidate SNPs, which can be applied as genetic markers for genome wide genetic studies. AVAILABILITY: The stand-alone version of MAVIANT program for local use is freely available under GPL license terms at http://snp.agrsci.dk/maviant. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. AU - Panitz, F AU - Stengaard, H AU - Hornshøj, H AU - Gorodkin, J AU - Hedegaard, J AU - Cirera, S AU - Thomsen, B AU - Madsen, LB AU - Høj, A AU - Vingborg, RK AU - Zahn, B AU - Wang, X AU - Wang, X AU - Wernersson, R AU - Jørgensen, CB AU - Scheibye-Knudsen, K AU - Arvin, T AU - Lumholdt, S AU - Sawera, M AU - Green, T AU - Nielsen, BJ AU - Havgaard, JH AU - Brunak, S AU - Fredholm, M AU - Bendixen, C PY - 2007/07/01/ UR - http://view.ncbi.nlm.nih.gov/pubmed/17646321 ER -