SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation
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SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation. / Panitz, Frank; Stengaard, Henrik; Hornshøj, Henrik; Gorodkin, Jan; Hedegaard, Jakob; Cirera, Susanna; Thomsen, Bo Stjerne; Madsen, Lone B; Høj, Anette; Vingborg, Rikke; Zahn, Bujie; Wang, Xuegang; Wang, Xuefei; Wernersson, Rasmus; Jørgensen, Claus B; Scheibye-Knudsen, Karsten; Arvin, Troels; Lumholdt, Steen; Sawera, Milena; Green, Trine; Nielsen, Bente; Havgaard, Jakob H; Brunak, Søren; Fredholm, Merete; Bendixen, Christian.
In: Bioinformatics, Vol. 23, No. 13, 2007, p. i387-91.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation
AU - Panitz, Frank
AU - Stengaard, Henrik
AU - Hornshøj, Henrik
AU - Gorodkin, Jan
AU - Hedegaard, Jakob
AU - Cirera, Susanna
AU - Thomsen, Bo Stjerne
AU - Madsen, Lone B
AU - Høj, Anette
AU - Vingborg, Rikke
AU - Zahn, Bujie
AU - Wang, Xuegang
AU - Wang, Xuefei
AU - Wernersson, Rasmus
AU - Jørgensen, Claus B
AU - Scheibye-Knudsen, Karsten
AU - Arvin, Troels
AU - Lumholdt, Steen
AU - Sawera, Milena
AU - Green, Trine
AU - Nielsen, Bente
AU - Havgaard, Jakob H
AU - Brunak, Søren
AU - Fredholm, Merete
AU - Bendixen, Christian
PY - 2007
Y1 - 2007
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 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 http://snp.agrsci.dk/maviantContact: christian.bendixen@agrsci.dkSupplementary information: Supplementary data are available at Bioinformatics online.
AB - 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 http://snp.agrsci.dk/maviantContact: christian.bendixen@agrsci.dkSupplementary information: Supplementary data are available at Bioinformatics online.
KW - Algorithms
KW - Animals
KW - Computer Graphics
KW - DNA Mutational Analysis
KW - Database Management Systems
KW - Databases, Genetic
KW - Documentation
KW - Expressed Sequence Tags
KW - Information Storage and Retrieval
KW - Polymorphism, Single Nucleotide
KW - Sequence Alignment
KW - Sequence Analysis, DNA
KW - Software
KW - Swine
KW - User-Computer Interface
U2 - 10.1093/bioinformatics/btm192
DO - 10.1093/bioinformatics/btm192
M3 - Journal article
C2 - 17646321
VL - 23
SP - i387-91
JO - Computer Applications in the Biosciences
JF - Computer Applications in the Biosciences
SN - 1471-2105
IS - 13
ER -
ID: 8078759