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

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

doi:10.1093/bioinformatics/btm192

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

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

26 Citations (Scopus)

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 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/maviant
Contact: [email protected]
Supplementary information: Supplementary data are available at Bioinformatics online.

Original language	English
Journal	Bioinformatics
Volume	23
Issue number	13
Pages (from-to)	i387-91
Number of pages	5
ISSN	1367-4803
DOIs	https://doi.org/10.1093/bioinformatics/btm192
Publication status	Published - 2007

Keywords

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

Access to Document

10.1093/bioinformatics/btm192

Cite this

Panitz, F., Stengaard, H., Hornshøj, H., Gorodkin, J., Hedegaard, J., Cirera, S., Thomsen, B. S., Madsen, L. B., Høj, A., Vingborg, R., Zahn, B., Wang, X., Wang, X., Wernersson, R., Jørgensen, C. B., Scheibye-Knudsen, K., Arvin, T., Lumholdt, S., Sawera, M., ... Bendixen, C. (2007). SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation. Bioinformatics, 23(13), i387-91. https://doi.org/10.1093/bioinformatics/btm192

Panitz, F, Stengaard, H, Hornshøj, H, Gorodkin, J, Hedegaard, J, Cirera, S, Thomsen, BS, Madsen, LB, Høj, A, Vingborg, R, Zahn, B, Wang, X, Wang, X, Wernersson, R, Jørgensen, CB, Scheibye-Knudsen, K, Arvin, T, Lumholdt, S, Sawera, M, Green, T, Nielsen, B, Havgaard, JH , Brunak, S , Fredholm, M & Bendixen, C 2007, 'SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation', Bioinformatics, vol. 23, no. 13, pp. i387-91. https://doi.org/10.1093/bioinformatics/btm192

@article{be2efa20a1c211ddb6ae000ea68e967b,

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

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 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: [email protected] information: Supplementary data are available at Bioinformatics online.",

keywords = "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",

author = "Frank Panitz and Henrik Stengaard and Henrik Hornsh{\o}j and Jan Gorodkin and Jakob Hedegaard and Susanna Cirera and Thomsen, {Bo Stjerne} and Madsen, {Lone B} and Anette H{\o}j and Rikke Vingborg and Bujie Zahn and Xuegang Wang and Xuefei Wang and Rasmus Wernersson and J{\o}rgensen, {Claus B} and Karsten Scheibye-Knudsen and Troels Arvin and Steen Lumholdt and Milena Sawera and Trine Green and Bente Nielsen and Havgaard, {Jakob H} and S{\o}ren Brunak and Merete Fredholm and Christian Bendixen",

year = "2007",

doi = "10.1093/bioinformatics/btm192",

language = "English",

volume = "23",

pages = "i387--91",

journal = "Bioinformatics",

issn = "1367-4803",

publisher = "Oxford University Press",

number = "13",

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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: [email protected] 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: [email protected] 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

SN - 1367-4803

VL - 23

SP - i387-91

JO - Bioinformatics

JF - Bioinformatics

IS - 13

ER -

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

Abstract

Keywords

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