Hi - in the humsavar dataset there are variants given by protein position and amino acid change. http://www.uniprot.org/docs/humsavar
Is there a way to convert these to chromosome positions and nucleotide changes? thanks.
I should probably add for clarification that some snps listed to do not have an rsid. this is a particularly challenging case because i am not able to join to UCSC snp tracks via rsid (where chromosomal positions exist)
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arronslacey
This file (humsavar.txt) is complemented by files of amino acid altering variants imported from Ensembl Variation databases. Mapped sequence variants are supplied per species in a tab delimited text file.ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/variants/
In particular, the human file is homo_sapiens_variation.txt.gz: The variants listed are the Ensembl Variation databases' set of 1000 Genomes project (http://www.1000genomes.org/) and Catalogue of Somatic Mutations In Cancer (COSMIC) v71, imported directly from COSMIC and via Ensembl Variation, protein altering variants (SO:0001583). COSMIC v71 variants are the last freely available somatic variants from COSMIC before their licence change; therefore the accuracy of the information provided for a COSMIC variant should be verified with COSMIC. (Text from README file in that directory)
Please don't hesitate to contact the UniProt helpdesk in case of questions about these files.
Thanks Elisabeth - very helpful! I had also looked into the Bisoconductor package VariantAnnotation that includes data objects such as polyPhen.Hsapiens.dbSNP131 - which maps most of the rsids to the humsavar dataset. it's obviously a bit out of date now so I much appreciate alternative data scourses that you mentioned.
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