Dear all
I have get a list of SNP numbers and their position. I would like to know the specific information , like the original nucleotide, allele change information and residue change information from dbSNPs ftp server especially the latter two.
For example, rs268 : original nucleotide : A ; Allele change : AAT ⇒ AGT ; Residue change : N [Asn] ⇒ S [Ser]
It's easy to search only one on dbSNPs other than many. Is there any files in ftp.ncbi.nih.gov server that contain my requirements for me to match my SNPs with allele change information and residue change information by using SNP numbers ?
I hava tried hard to search. For too many files, I couldn't find the file I need.
Thank you a lot.
2 answers
Is it a requirement to use data from the dbSNP FTP site?
I believe the Ensembl Variant Effect Predictor (VEP) tool should do what you need. Either the web based version or the stand alone PERL script. It can take a list of rsIDs as input and provides lots of useful output including allele and residue change. You may have to tweak the settings or use a custom script to select just the output info you are interested in
Follow the instructutions here http://www.ensembl.org/info/docs/variation/vep/index.html#web
Hope that helps!
Exploit snpEff (http://snpeff.sourceforge.net/), you will find it useful.
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This does not directly answer your question, but you could use NCBI EUtils. For many rsIDs, a biopython solution could be built along these lines: http://www.biostars.org/post/show/12235/find-amino-acid-change-for-snp-using-eutils/