List of SNP's for alleles at a particular locus

Question

[emmapead2]

Hi there!

I've been given a list of alleles of a particular gene locus and need to generate a list of SNP's for that locus. So that I would have a file that contains this [GGAT/CAGC....etc]. Does anyone know of any software that would let me do this?

It have the nucleotide sequences in Fasta format.

[Sean Davis]

Could you show us what your input data is and, specifically, what you want the output to be? I suspect that you'll want to write some quick software yourself, but it will only be clear with a bit more detail.

[emmapead2]

I only have the nucleotide fasta files which I got from NCBI.

[Sean Davis]

So, you have nucleotide fasta files. Where are you getting the "alleles" that you need to extract?

[emmapead2]

So the fasta files are the sequences of the different alleles at a particular locus. So I need to look for SNP's in this locus for each allele. So SNP's in each allele sequence.

Answer 1

[emmapead2]

So the fasta files are the sequences of the different alleles at a particular locus. So I need to look for SNP's in this locus for each allele. So SNP's in each allele sequence.

[Ibrahim Tanyalcin]

Dear emmapead2,

Did you try using the biomart from ensembl? (http://www.ensembl.org/biomart) Here you can choose the Homo Sapiens short variants from dataset tab and then enter the specific loci you have in the filters section (choose the multiple chromosomal regions).

I hope this helps

[emmapead2]

Thanks very much! I actually found a nice piece of code that did the trick: snp-sites