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Protocols

SNPMeta specifications

Information


Unique identifier OMICS_01923
Name SNPMeta
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data A DNA sequence.
Input format FASTA
Output format TSV
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python, Shell (Bash)
Computer skills Advanced
Version 2.0
Stability Stable
Requirements
MacOS, Biopython, EMBOSS
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Download


download.png

Versioning


No version available

Maintainer


  • person_outline Peter Morrell

Additional information


A previous version can be found at https://github.com/pmorrell/SNPMeta

Information


Unique identifier OMICS_01923
Name SNPMeta
Interface Web user interface
Restrictions to use None
Input data A file of SNP to annotate.
Input format FASTA
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Maintainer


  • person_outline Peter Morrell

Additional information


A previous version can be found at https://github.com/pmorrell/SNPMeta

Publication for SNPMeta

SNPMeta citations

 (4)
library_books

Genome wide meta analysis of 241,258 adults accounting for smoking behaviour identifies novel loci for obesity traits

2017
Nat Commun
PMCID: 5414044
PMID: 28443625
DOI: 10.1038/ncomms14977

[…] crease in smoking quantity of 10 cigarettes per day. There were 10,058 Never smokers, 13,418 Ever smokers, 11,796 Non-current smokers, 6,966 Current smokers and 11,436 samples with the SQ phenotypes. SNPMETA was used to perform an inverse-variance weighted fixed effects meta-analysis across cohorts at all SNPs in each region, and included a single GC correction. At each SNP, only those cohorts tha […]

library_books

Application of next generation sequencing technology to study genetic diversity and identify unique SNP markers in bread wheat from Kazakhstan

2014
BMC Plant Biol
PMCID: 4180858
PMID: 25928569
DOI: 10.1186/s12870-014-0258-7

[…] onfidence SNP markers were reported and used for studying of the genome evolution, genetic diversity and geographic origin of various accessions [,-]. Bioinformatics databases including CerealsDB and SNPMeta provide publicly accessible data on NGS-SNP, GBS and KASPar technology [,].The aims of the current study were: (1) assess the suitability of the SNP platforms to explore the origins and basis […]

library_books

Two Genomic Regions Contribute Disproportionately to Geographic Differentiation in Wild Barley

2014
PMCID: 4455769
PMID: 24760390
DOI: 10.1534/g3.114.010561

[…] d based on the consensus genetic map of . In the inbred WBDC lines, observed heterozygosity was extremely low (0.2%), thus we treat the data as haploid genotypes.SNPs were annotated using the program SNPMeta (). Annotation for each SNP included GenBank ID, gene short name, whether the SNP occurs in coding or noncoding sequence, the SNP position within a codon, and determination of whether the SNP […]

call_split

Comparative Analyses Identify the Contributions of Exotic Donors to Disease Resistance in a Barley Experimental Population

2013
PMCID: 3815057
PMID: 24048643
DOI: 10.1534/g3.113.007294
call_split See protocol

[…] on the consensus genetic map of and are depicted in Supporting Information, Figure S1.SNPs were annotated to determine the genes of origin. Annotations were performed using the SNP annotation tool, SNPMeta (T. Y. Kono, K. Seth, J. A. Poland, and P. L. Morrell, in press) based on the contextual sequence used for the Illumina SNP assay design (). SNP contextual sequences were used as BLAST queries […]

Citations

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SNPMeta institution(s)
Department of Agronomy & Plant Genetics, University of Minnesota, St. Paul, MN, USA; Hard Winter Wheat Genetics Research Unit, USDA ARS, Kansas State University, Manhattan, KS, USA; Department of Agronomy, Kansas State University, Manhattan, KS, USA
SNPMeta funding source(s)
Supported by the US Department of Agriculture (USDA); partly by the US National Institute for Food and Agriculture (NIFA) (2011-68002-30029); a USDA National Needs Fellowship (USDA NIFA 2011-38420-20068) and in part by the USDA - Agricultural Research Service (Appropriation No. 5430-21000-006-00D) and Kansas State University.

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