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

Research output: Contribution to journalJournal articleResearchpeer-review

  • Frank Panitz
  • Henrik Stengaard
  • Henrik Hornshøj
  • Jakob Hedegaard
  • Susanna Cirera
  • Bo Stjerne Thomsen
  • Lone B Madsen
  • Anette Høj
  • Rikke Vingborg
  • Bujie Zahn
  • Xuegang Wang
  • Xuefei Wang
  • Rasmus Wernersson
  • Karsten Scheibye-Knudsen
  • Troels Arvin
  • Steen Lumholdt
  • Milena Sawera
  • Trine Green
  • Bente Nielsen
  • Christian Bendixen

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 candicate 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
Supplementary information: Supplementary data are available at Bioinformatics online.

Original languageEnglish
Issue number13
Pages (from-to)i387-91
Number of pages5
Publication statusPublished - 2007

    Research areas

  • Algorithms, Animals, Computer Graphics, DNA Mutational Analysis, Database Management Systems, Databases, Genetic, Documentation, Expressed Sequence Tags, Information Storage and Retrieval, Polymorphism, Single Nucleotide, Sequence Alignment, Sequence Analysis, DNA, Software, Swine, User-Computer Interface

ID: 8078759