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Protocols

SNPchiMp specifications

Information


Unique identifier OMICS_08305
Name SNPchiMp
Restrictions to use None
Database management system MySQL
Version 3.0
Maintained Yes

Taxon


  • Mammals
    • Bos taurus

Maintainer


  • person_outline Ezequiel L. Nicolazzi

Publications for SNPchiMp

SNPchiMp citations

 (5)
library_books

Using genome wide association studies to identify common QTL regions in three different genetic backgrounds based on Iberian pig breed

2018
PLoS One
PMCID: 5844516
PMID: 29522525
DOI: 10.1371/journal.pone.0190184

[…] ing GenABEL package [] in R environment, and polymorphisms with a minimum allele frequency (MAF) < 0.05 were discarded for further analysis. In order to be able to compare data from the two platforms SNPchiMp v.3 [] was used to select SNPs overlapping between both. […]

library_books

Systems genomics study reveals expression quantitative trait loci, regulator genes and pathways associated with boar taint in pigs

2018
PLoS One
PMCID: 5811030
PMID: 29438444
DOI: 10.1371/journal.pone.0192673

[…] osomes, were obtained by the R package biomaRt (v. 2.30.0) [, ] from the Sus scrofa genome build (10.2, version 79). The chromosomal locations of the SNPs associated with the eQTLs were obtained from SNPchiMp (v. 3) database []. The chromosomal densities of eQTLs were calculated by the number of either unfiltered or filtered eQTLs per chromosome divided by length in bases of the respective chromos […]

call_split

Identification of Candidate Genes for Reactivity in Guzerat (Bos indicus) Cattle: A Genome Wide Association Study

2017
PLoS One
PMCID: 5268462
PMID: 28125592
DOI: 10.1371/journal.pone.0169163
call_split See protocol

[…] Map positions of the SNPs were based on UMD3.1. Information about the markers (rs, map position, alleles) were obtained using the SNPchiMp tool []. When these SNPs were located within a gene, several analyses were carried out. First, the position of the SNP (intronic or exonic, 5´-UTR or 3´-UTR) was determined. Second, repercuss […]

library_books

SNP and haplotype based genome wide association studies for growth, carcass, and meat quality traits in a Duroc multigenerational population

2016
BMC Genet
PMCID: 4837538
PMID: 27094516
DOI: 10.1186/s12863-016-0368-3

[…] cance thresholds defined by the Bonferroni correction was too conservative. Therefore, the genome-wide suggestive threshold was also defined as; P = 5.0 × 10−5. SNP maps were updated according to the SNPchiMp v.2 database [] and the Sscrofa 10.2 assembly. The positional candidate genes within the range of 1 Mb bin size of the significant region were scanned using the NCBI2R R-package []. r2 values […]

call_split

The Use of Kosher Phenotyping for Mapping QTL Affecting Susceptibility to Bovine Respiratory Disease

2016
PLoS One
PMCID: 4831767
PMID: 27077383
DOI: 10.1371/journal.pone.0153423
call_split See protocol

[…] The SNPchiMp database [] was used to convert the Illumina SNP name to the rsID (the SNP accession number used to search a SNP in all public databases). The rsID was used in NCBI database (http://www.ncbi. […]

Citations

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SNPchiMp institution(s)
Bioinformatics and Biostatistical Genomics group, Fondazione Parco Tecnologico Padano, Via Einstein, Loc Cascina Codazza, Lodi, Italy

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