SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation - PubMed (original) (raw)
. 2007 Jul 1;23(13):i387-91.
doi: 10.1093/bioinformatics/btm192.
Henrik Stengaard, Henrik Hornshøj, Jan Gorodkin, Jakob Hedegaard, Susanna Cirera, Bo Thomsen, Lone B Madsen, Anette Høj, Rikke K Vingborg, Bujie Zahn, Xuegang Wang, Xuefei Wang, Rasmus Wernersson, Claus B Jørgensen, Karsten Scheibye-Knudsen, Troels Arvin, Steen Lumholdt, Milena Sawera, Trine Green, Bente J Nielsen, Jakob H Havgaard, Søren Brunak, Merete Fredholm, Christian Bendixen
Affiliations
- PMID: 17646321
- DOI: 10.1093/bioinformatics/btm192
SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation
Frank Panitz et al. Bioinformatics. 2007.
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 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.
Availability: The stand-alone version of MAVIANT program for local use is freely available under GPL license terms at http://snp.agrsci.dk/maviant.
Supplementary information: Supplementary data are available at Bioinformatics online.
Similar articles
- LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources.
Karchin R, Diekhans M, Kelly L, Thomas DJ, Pieper U, Eswar N, Haussler D, Sali A. Karchin R, et al. Bioinformatics. 2005 Jun 15;21(12):2814-20. doi: 10.1093/bioinformatics/bti442. Epub 2005 Apr 12. Bioinformatics. 2005. PMID: 15827081 - MSQT for choosing SNP assays from multiple DNA alignments.
Warthmann N, Fitz J, Weigel D. Warthmann N, et al. Bioinformatics. 2007 Oct 15;23(20):2784-7. doi: 10.1093/bioinformatics/btm428. Epub 2007 Sep 4. Bioinformatics. 2007. PMID: 17785349 - SNP-PHAGE--High throughput SNP discovery pipeline.
Matukumalli LK, Grefenstette JJ, Hyten DL, Choi IY, Cregan PB, Van Tassell CP. Matukumalli LK, et al. BMC Bioinformatics. 2006 Oct 23;7:468. doi: 10.1186/1471-2105-7-468. BMC Bioinformatics. 2006. PMID: 17059604 Free PMC article. - Computational prediction of the effects of non-synonymous single nucleotide polymorphisms in human DNA repair genes.
Nakken S, Alseth I, Rognes T. Nakken S, et al. Neuroscience. 2007 Apr 14;145(4):1273-9. doi: 10.1016/j.neuroscience.2006.09.004. Epub 2006 Oct 19. Neuroscience. 2007. PMID: 17055652 Review. - Single nucleotide polymorphism hunting in cyberspace.
Gu Z, Hillier L, Kwok PY. Gu Z, et al. Hum Mutat. 1998;12(4):221-5. doi: 10.1002/(SICI)1098-1004(1998)12:4<221::AID-HUMU1>3.0.CO;2-I. Hum Mutat. 1998. PMID: 9744471 Review.
Cited by
- Seq4SNPs: new software for retrieval of multiple, accurately annotated DNA sequences, ready formatted for SNP assay design.
Field HI, Scollen SA, Luccarini C, Baynes C, Morrison J, Dunning AM, Easton DF, Pharoah PD. Field HI, et al. BMC Bioinformatics. 2009 Jun 12;10:180. doi: 10.1186/1471-2105-10-180. BMC Bioinformatics. 2009. PMID: 19523221 Free PMC article. - The Neonatal and Juvenile Pig in Pediatric Drug Discovery and Development.
Ayuso M, Buyssens L, Stroe M, Valenzuela A, Allegaert K, Smits A, Annaert P, Mulder A, Carpentier S, Van Ginneken C, Van Cruchten S. Ayuso M, et al. Pharmaceutics. 2020 Dec 30;13(1):44. doi: 10.3390/pharmaceutics13010044. Pharmaceutics. 2020. PMID: 33396805 Free PMC article. Review. - AlignMiner: a Web-based tool for detection of divergent regions in multiple sequence alignments of conserved sequences.
Guerrero D, Bautista R, Villalobos DP, Cantón FR, Claros MG. Guerrero D, et al. Algorithms Mol Biol. 2010 Jun 2;5:24. doi: 10.1186/1748-7188-5-24. Algorithms Mol Biol. 2010. PMID: 20525162 Free PMC article. - Mining for single nucleotide polymorphisms in pig genome sequence data.
Kerstens HH, Kollers S, Kommadath A, Del Rosario M, Dibbits B, Kinders SM, Crooijmans RP, Groenen MA. Kerstens HH, et al. BMC Genomics. 2009 Jan 6;10:4. doi: 10.1186/1471-2164-10-4. BMC Genomics. 2009. PMID: 19126189 Free PMC article. - An approach to identify SNPs in the gene encoding acetyl-CoA acetyltransferase-2 (ACAT-2) and their proposed role in metabolic processes in pig.
Sodhi SS, Ghosh M, Song KD, Sharma N, Kim JH, Kim NE, Lee SJ, Kang CW, Oh SJ, Jeong DK. Sodhi SS, et al. PLoS One. 2014 Jul 22;9(7):e102432. doi: 10.1371/journal.pone.0102432. eCollection 2014. PLoS One. 2014. PMID: 25050817 Free PMC article.
Publication types
MeSH terms
LinkOut - more resources
Full Text Sources
Research Materials