I have some gene sequences, retrieved from GWAS study and want to know the SNP variant is present in which site. Any tool is there which remark the boundries like regulatory, intron and exon regions in these gene sequence. Any help...
If it is an already published SNP, you may find that info on the GWAS Catalog, in the context column.
But this is a rice SNP....
Snpeff (http://snpeff.sourceforge.net/) may be what you are looking for. You can see the available databases as:
java -jar snpEff.jar databases | grep -wi "rice"
It will annotate as intron/exon/ and even synonymous, non, stop-gained, etc. assuming your version of rice is available.
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