title: SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation.
abstract: BACKGROUND
  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.
  
  
  BACKGROUND
  The stand-alone version of MAVIANT program for local use is freely available under GPL license terms at http://snp.agrsci.dk/maviant.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, University of Aarhus, DK-8830 Tjele, Denmark.
authors.forename: Frank
authors.initials: F
authors.lastname: Panitz
authors.forename: Henrik
authors.initials: H
authors.lastname: Stengaard
authors.forename: Henrik
authors.initials: H
authors.lastname: Hornshøj
authors.forename: Jan
authors.initials: J
authors.lastname: Gorodkin
authors.forename: Jakob
authors.initials: J
authors.lastname: Hedegaard
authors.forename: Susanna
authors.initials: S
authors.lastname: Cirera
authors.forename: Bo
authors.initials: B
authors.lastname: Thomsen
authors.forename: Lone B
authors.initials: LB
authors.lastname: Madsen
authors.forename: Anette
authors.initials: A
authors.lastname: Høj
authors.forename: Rikke K
authors.initials: RK
authors.lastname: Vingborg
authors.forename: Bujie
authors.initials: B
authors.lastname: Zahn
authors.forename: Xuegang
authors.initials: X
authors.lastname: Wang
authors.forename: Xuefei
authors.initials: X
authors.lastname: Wang
authors.forename: Rasmus
authors.initials: R
authors.lastname: Wernersson
authors.forename: Claus B
authors.initials: CB
authors.lastname: Jørgensen
authors.forename: Karsten
authors.initials: K
authors.lastname: Scheibye-Knudsen
authors.forename: Troels
authors.initials: T
authors.lastname: Arvin
authors.forename: Steen
authors.initials: S
authors.lastname: Lumholdt
authors.forename: Milena
authors.initials: M
authors.lastname: Sawera
authors.forename: Trine
authors.initials: T
authors.lastname: Green
authors.forename: Bente J
authors.initials: BJ
authors.lastname: Nielsen
authors.forename: Jakob H
authors.initials: JH
authors.lastname: Havgaard
authors.forename: Søren
authors.initials: S
authors.lastname: Brunak
authors.forename: Merete
authors.initials: M
authors.lastname: Fredholm
authors.forename: Christian
authors.initials: C
authors.lastname: Bendixen
mesh_terms: D000465:Algorithms; D000818:Animals; D003196:Computer Graphics; D004252:DNA Mutational Analysis / Q000379:methods*; D003628:Database Management Systems; D030541:Databases, Genetic; D004282:Documentation / Q000379:methods*; D020224:Expressed Sequence Tags; D016247:Information Storage and Retrieval; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software; D013552:Swine; D014584:User-Computer Interface