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Bioinformatics 2007 23(13):i387-i391; doi:10.1093/bioinformatics/btm192
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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

Frank Panitz 1, Henrik Stengaard 1, Henrik Hornshøj 1, Jan Gorodkin 2, Jakob Hedegaard 1, Susanna Cirera 2, Bo Thomsen 1, Lone B. Madsen 1, Anette Høj 1, Rikke K. Vingborg 1, Bujie Zahn 1, Xuegang Wang 1, Xuefei Wang 1, Rasmus Wernersson 3, Claus B. Jørgensen 2, Karsten Scheibye-Knudsen 2, Troels Arvin 2, Steen Lumholdt 2, Milena Sawera 2, Trine Green 2, Bente J. Nielsen 2, Jakob H. Havgaard 2, Søren Brunak 3, Merete Fredholm 2 and Christian Bendixen 1,*

1Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, University of Aarhus, DK-8830 Tjele, 2Department of Basic Animal and Veterinary Sciences, Faculty of Life Sciences, University of Copenhagen, DK-1870 Frederiksberg C and 3Center for Biological Sequence Analysis, BioCentrum-DTU, Building 208, DK-2800 Lyngby, Denmark

*To whom correspondence should be addressed.


  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.

Contact: christian.bendixen{at}agrsci.dk

Supplementary information: Supplementary data are available at Bioinformatics online.


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