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
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Ram
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Ibrahim Tanyalcin
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Ibrahim Tanyalcin
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.
I only have the nucleotide fasta files which I got from NCBI.
So, you have nucleotide fasta files. Where are you getting the "alleles" that you need to extract?
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.