Human Genome Mutation Search Database

Question

[Gao Wang]

Dear All,

I am looking for a database that gives me information of mutations across human genome. Supposedly it works like this: I submit a file containing the genomic physical locations of a bunch of mutations I am interested in, and I get reply from the database telling me the type of each mutation, i.e. synonymous, frame shift, missense or nonsynonymous. Could you suggest such a database?

Thank you.

Kindest regards, Gao

PS: the interest is ANY real single base mutation, not confined to SNPs, and not predicted by tools like Polyphen

[Khader Shameer]

Have you tried : HGMD : Human Gene Mutation Database?

[Gao Wang]

Thanks Khader, this looks a hopeful one! I'll dig into it.

Answer 1

[Paulo Nuin]

Have you tried Cosmic? dbSNP? HapMap? All of them will give some type of result, maybe you will get what you need directly, maybe you will need to parse and analyse it.

[Gao Wang]

Thanks Paulo, yet indeed those databases give only certain type of result (common mutations like SNPs or genes) while I am interested in functional consequence of (potentially many) any single nucleotide mutation across human genome. Also as you said I may need scripts to communicate with some database in order to extract such information in "batch mode".

[Paulo Nuin]

There's no free lunch out there!