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SNPM eta: SNP annotation and SNP metadata collection without a reference genome
Author(s) -
Kono Thomas J. Y.,
Seth Kiran,
Poland Jesse A.,
Morrell Peter L.
Publication year - 2014
Publication title -
molecular ecology resources
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.96
H-Index - 136
eISSN - 1755-0998
pISSN - 1755-098X
DOI - 10.1111/1755-0998.12183
Subject(s) - biology , single nucleotide polymorphism , reference genome , snp , snp genotyping , genome , genotyping , genbank , annotation , computational biology , dbsnp , genetics , tag snp , gene , genotype
The increase in availability of resequencing data is greatly accelerating SNP discovery and has facilitated the development of SNP genotyping assays. This, in turn, is increasing interest in annotation of individual SNP s. Currently, these data are only available through curation, or comparison to a reference genome. Many species lack a reference genome, but are still important genetic models or are significant species in agricultural production or natural ecosystems. For these species, it is possible to annotate SNP s through comparison with cDNA , or data from well‐annotated genes in public repositories. We present SNPM eta, a tool which gathers information about SNPs by comparison with sequences present in GenBank databases. SNPM eta is able to annotate SNPs from contextual sequence in SNP assay designs, and SNPs discovered through genotyping by sequencing ( GBS ) approaches. However, SNP s discovered through GBS occur throughout the genome, rather than only in gene space, and therefore do not annotate at high rates. SNPM eta can therefore be used to annotate SNP s in nonmodel species or species that lack a reference genome. Annotations generated by SNPM eta are highly concordant with annotations that would be obtained from a reference genome.