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Type: Journal article
Title: SNPchiMp v.3: integrating and standardizing single nucleotide polymorphism data for livestock species
Author: Nicolazzi, E.
Caprera, A.
Nazzicari, N.
Cozzi, P.
Strozzi, F.
Lawley, C.
Pirani, A.
Soans, C.
Brew, F.
Jorjani, H.
Evans, G.
Simpson, B.
Tosser-Klopp, G.
Brauning, R.
Williams, J.
Stella, A.
Citation: BMC Genomics, 2015; 16(1):283-1-283-6
Publisher: BioMed Central
Issue Date: 2015
ISSN: 1471-2164
Statement of
Ezequiel L Nicolazzi, Andrea Caprera, Nelson Nazzicari, Paolo Cozzi, Francesco Strozzi, Cindy Lawley, Ali Pirani, Chandrasen Soans, Fiona Brew, Hossein Jorjani, Gary Evans, Barry Simpson, Gwenola Tosser-Klopp, Rudiger Brauning, John L Williams and Alessandra Stella
Abstract: In recent years, the use of genomic information in livestock species for genetic improvement, association studies and many other fields has become routine. In order to accommodate different market requirements in terms of genotyping cost, manufacturers of single nucleotide polymorphism (SNP) arrays, private companies and international consortia have developed a large number of arrays with different content and different SNP density. The number of currently available SNP arrays differs among species: ranging from one for goats to more than ten for cattle, and the number of arrays available is increasing rapidly. However, there is limited or no effort to standardize and integrate array- specific (e.g. SNP IDs, allele coding) and species-specific (i.e. past and current assemblies) SNP information.Here we present SNPchiMp v.3, a solution to these issues for the six major livestock species (cow, pig, horse, sheep, goat and chicken). Original data was collected directly from SNP array producers and specific international genome consortia, and stored in a MySQL database. The database was then linked to an open-access web tool and to public databases. SNPchiMp v.3 ensures fast access to the database (retrieving within/across SNP array data) and the possibility of annotating SNP array data in a user-friendly fashion.This platform allows easy integration and standardization, and it is aimed at both industry and research. It also enables users to easily link the information available from the array producer with data in public databases, without the need of additional bioinformatics tools or pipelines. In recognition of the open-access use of Ensembl resources, SNPchiMp v.3 was officially credited as an Ensembl E!mpowered tool. Availability at
Keywords: SNP; Array; Illumina; Affymetrix; GeneSeek; Integration; Standardization; Imputation; Ensembl; NCBI
Description: Published: 10 April 2015
Rights: © Nicolazzi et al.; licensee BioMed Central. 2015 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://​creativecommons.​org/​licenses/​by/​4.​0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://​creativecommons.​org/​publicdomain/​zero/​1.​0/​) applies to the data made available in this article, unless otherwise stated.
DOI: 10.1186/s12864-015-1497-1
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Appears in Collections:Animal and Veterinary Sciences publications
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