SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation.
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.
Panitz
Frank
F
Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, University of Aarhus, DK-8830 Tjele, Denmark.
Stengaard
Henrik
H
Hornshøj
Henrik
H
Gorodkin
Jan
J
Hedegaard
Jakob
J
Cirera
Susanna
S
Thomsen
Bo
B
Madsen
Lone B
LB
Høj
Anette
A
Vingborg
Rikke K
RK
Zahn
Bujie
B
Wang
Xuegang
X
Wang
Xuefei
X
Wernersson
Rasmus
R
Jørgensen
Claus B
CB
Scheibye-Knudsen
Karsten
K
Arvin
Troels
T
Lumholdt
Steen
S
Sawera
Milena
M
Green
Trine
T
Nielsen
Bente J
BJ
Havgaard
Jakob H
JH
Brunak
Søren
S
Fredholm
Merete
M
Bendixen
Christian
C
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