Question: generating database of SNPs from multiple alignment?
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gravatar for gemmcam
4.0 years ago by
gemmcam0
gemmcam0 wrote:

Sorry if this is really obvious, i'm really new to Bioinformatics.  I have a list of alleles from MHC2, all with accession numbers (theres 18) I downloaded the FASTA sequences for these and did a multiple alignment of them using ClustalX.  I now need to generate a database of SNPs for each one and add frequencies etc, and I am a little confused on how to do this.  I can see differences in the alignments but not everyone of these differences would necessarily be a SNP right? Is there a program that will take the alignment data and give me a list of SNPs for each allele or is there another way I could be doing this?  

 

Thanks.

 

Gemma

snp alignment • 879 views
ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by gemmcam0

Hi Gemmcam - If you are using publically available data, and not your own data, then why not just get the SNPs from a publically available database? Could you help us understand a bit more what you are doing? If so, I can likely answer this question.

ADD REPLYlink written 4.0 years ago by Vincent Laufer1.1k
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