generating database of SNPs from multiple alignment?

Question

[gemmcam]

Sorry if this is really obvious, I'm really new to Bioinformatics. I have a list of alleles from MHC2, all with accession numbers (there's 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

[LauferVA]

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.