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NovelSNPer: A Fast Tool for the Identification and Characterization of Novel SNPs and InDels

Typically, next-generation resequencing projects produce large lists of variants. NovelSNPer is a software tool that permits fast and efficient processing of such output lists. In a first step, NovelSNPer determines if a variant represents a known variant or a previously unknown variant. In a second...

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Detalles Bibliográficos
Autores principales: Aßmus, Jens, Schmitt, Armin O., Bortfeldt, Ralf H., Brockmann, Gudrun A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Hindawi Publishing Corporation 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3206323/
https://www.ncbi.nlm.nih.gov/pubmed/22110502
http://dx.doi.org/10.1155/2011/657341
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author Aßmus, Jens
Schmitt, Armin O.
Bortfeldt, Ralf H.
Brockmann, Gudrun A.
author_facet Aßmus, Jens
Schmitt, Armin O.
Bortfeldt, Ralf H.
Brockmann, Gudrun A.
author_sort Aßmus, Jens
collection PubMed
description Typically, next-generation resequencing projects produce large lists of variants. NovelSNPer is a software tool that permits fast and efficient processing of such output lists. In a first step, NovelSNPer determines if a variant represents a known variant or a previously unknown variant. In a second step, each variant is classified into one of 15 SNP classes or 19 InDel classes. Beside the classes used by Ensembl, we introduce POTENTIAL_START_GAINED and START_LOST as new functional classes and present a classification scheme for InDels. NovelSNPer is based upon the gene structure information stored in Ensembl. It processes two million SNPs in six hours. The tool can be used online or downloaded.
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spelling pubmed-32063232011-11-22 NovelSNPer: A Fast Tool for the Identification and Characterization of Novel SNPs and InDels Aßmus, Jens Schmitt, Armin O. Bortfeldt, Ralf H. Brockmann, Gudrun A. Adv Bioinformatics Research Article Typically, next-generation resequencing projects produce large lists of variants. NovelSNPer is a software tool that permits fast and efficient processing of such output lists. In a first step, NovelSNPer determines if a variant represents a known variant or a previously unknown variant. In a second step, each variant is classified into one of 15 SNP classes or 19 InDel classes. Beside the classes used by Ensembl, we introduce POTENTIAL_START_GAINED and START_LOST as new functional classes and present a classification scheme for InDels. NovelSNPer is based upon the gene structure information stored in Ensembl. It processes two million SNPs in six hours. The tool can be used online or downloaded. Hindawi Publishing Corporation 2011 2011-10-31 /pmc/articles/PMC3206323/ /pubmed/22110502 http://dx.doi.org/10.1155/2011/657341 Text en Copyright © 2011 Jens Aßmus et al. https://creativecommons.org/licenses/by/3.0/ This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Aßmus, Jens
Schmitt, Armin O.
Bortfeldt, Ralf H.
Brockmann, Gudrun A.
NovelSNPer: A Fast Tool for the Identification and Characterization of Novel SNPs and InDels
title NovelSNPer: A Fast Tool for the Identification and Characterization of Novel SNPs and InDels
title_full NovelSNPer: A Fast Tool for the Identification and Characterization of Novel SNPs and InDels
title_fullStr NovelSNPer: A Fast Tool for the Identification and Characterization of Novel SNPs and InDels
title_full_unstemmed NovelSNPer: A Fast Tool for the Identification and Characterization of Novel SNPs and InDels
title_short NovelSNPer: A Fast Tool for the Identification and Characterization of Novel SNPs and InDels
title_sort novelsnper: a fast tool for the identification and characterization of novel snps and indels
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3206323/
https://www.ncbi.nlm.nih.gov/pubmed/22110502
http://dx.doi.org/10.1155/2011/657341
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