title: SNPchiMp v.3: integrating and standardizing single nucleotide polymorphism data for livestock species.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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 http://bioinformatics.tecnoparco.org/SNPchimp.
authors.affiliation: Bioinformatics and Biostatistical Genomics group, Fondazione Parco Tecnologico Padano, Via Einstein, Loc. Cascina Codazza, 26900, Lodi, Italy. ezequiel.nicolazzi@tecnoparco.org.
authors.forename: Ezequiel L
authors.initials: EL
authors.lastname: Nicolazzi
authors.affiliation: Bioinformatics and Biostatistical Genomics group, Fondazione Parco Tecnologico Padano, Via Einstein, Loc. Cascina Codazza, 26900, Lodi, Italy. andrea.caprera@tecnoparco.org.
authors.forename: Andrea
authors.initials: A
authors.lastname: Caprera
authors.affiliation: Bioinformatics and Biostatistical Genomics group, Fondazione Parco Tecnologico Padano, Via Einstein, Loc. Cascina Codazza, 26900, Lodi, Italy. nelson.nazzicari@tecnoparco.org.
authors.forename: Nelson
authors.initials: N
authors.lastname: Nazzicari
authors.affiliation: Bioinformatics and Biostatistical Genomics group, Fondazione Parco Tecnologico Padano, Via Einstein, Loc. Cascina Codazza, 26900, Lodi, Italy. paolo.cozzi@tecnoparco.org.
authors.forename: Paolo
authors.initials: P
authors.lastname: Cozzi
authors.affiliation: Bioinformatics and Biostatistical Genomics group, Fondazione Parco Tecnologico Padano, Via Einstein, Loc. Cascina Codazza, 26900, Lodi, Italy. francesco.strozzi@tecnoparco.org.
authors.forename: Francesco
authors.initials: F
authors.lastname: Strozzi
authors.affiliation: Illumina Inc, 5200 Illumina Way, San Diego, CA, 92121, USA. clawley@illumina.com.
authors.forename: Cindy
authors.initials: C
authors.lastname: Lawley
authors.affiliation: Affymetrix Inc, 3420 Central Expressway, Santa Clara, CA, 95051, USA. ali_pirani@affymetrix.com.
authors.forename: Ali
authors.initials: A
authors.lastname: Pirani
authors.affiliation: Illumina Inc, 5200 Illumina Way, San Diego, CA, 92121, USA. csoans@illumina.com.
authors.forename: Chandrasen
authors.initials: C
authors.lastname: Soans
authors.affiliation: Affymetrix UK Ltd, Mercury Park, Wycombe Lane, High Wycombe, HP10 0HH, UK. fiona_brew@affymetrix.com.
authors.forename: Fiona
authors.initials: F
authors.lastname: Brew
authors.affiliation: Interbull center, Uppsala, S-75007, Sweden. hossein.jorjani@slu.se.
authors.forename: Hossein
authors.initials: H
authors.lastname: Jorjani
authors.affiliation: GeneSeek, a Neogen Company, Auchincruive, Ayr KA6 5HU, Scotland, UK. g.evans@neogeneurope.com.
authors.forename: Gary
authors.initials: G
authors.lastname: Evans
authors.affiliation: GeneSeek, a Neogen Company, Lincoln, NE, 68504, USA. bsimpson@neogen.com.
authors.forename: Barry
authors.initials: B
authors.lastname: Simpson
authors.affiliation: Génétique, Physiologie et Systèmes d'Élevage, Institut National de la Recherche Agronomique & Ecole Nationale Vétérinaire de Toulouse & Ecole Nationale Supérieure Agronomique de Toulouse, Castanet-Tolosan, 31326, France. gwenola.tosser@toulouse.inra.fr.
authors.forename: Gwenola
authors.initials: G
authors.lastname: Tosser-Klopp
authors.affiliation: AgResearch, Invermay Agricultural Centre, PB 50034, Mosgiel, New Zealand. rudiger.brauning@agresearch.co.nz.
authors.forename: Rudiger
authors.initials: R
authors.lastname: Brauning
authors.affiliation: Bioinformatics and Biostatistical Genomics group, Fondazione Parco Tecnologico Padano, Via Einstein, Loc. Cascina Codazza, 26900, Lodi, Italy. john.williams@tecnoparco.org.
authors.forename: John L
authors.initials: JL
authors.lastname: Williams
authors.affiliation: Bioinformatics and Biostatistical Genomics group, Fondazione Parco Tecnologico Padano, Via Einstein, Loc. Cascina Codazza, 26900, Lodi, Italy. alessandra.stella@tecnoparco.org.|Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Via Einstein, Cascina Codazza, Lodi 26900, Italy. alessandra.stella@tecnoparco.org.
authors.forename: Alessandra
authors.initials: A
authors.lastname: Stella
mesh_terms: D000818:Animals; D002417:Cattle; D019295:Computational Biology; D030541:Databases, Genetic; D016678:Genome; D006041:Goats / Q000235:genetics; D020407:Internet; D020641:Polymorphism, Single Nucleotide; D013045:Species Specificity; D014584:User-Computer Interface