Question:Convert from ENSEMBL transcript id, start and end position of a variant to Uniprot/SwissProt/TreMBL id and position

Question

[rashmi.bangalore123]

Hi,

I am a Computer Science student working on a Human Mutation dataset that contains proteins Uniprot identifiers and the position of the mutation in the FASTA sequence.

I want to convert from ENSEMBL transcript ID and transcription Start and End positions to UNIPROT ID and corresponding Uniprot position.

I came across several tools such as BioMart, but I am not sure how to go about to achieve what I require. The documentation is overwhelming and the tool is not intuitive for a newbie like me.

Request you to point me how to get the conversion easily, preferably an online web interface.

Thanks in advance, Rashmi

Answer 1

[WouterDeCoster]

Here is a webinar about using biomart, will likely contain everything you need: http://www.ebi.ac.uk/training/online/course/ensembl-browser-webinar-series-2016/data-export-biomart

Answer 2

[Elisabeth Gasteiger]

You may also find the downloadable UniProtKB variant data useful: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/variants/

Have a look at the README file ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/variants/README

The files relevant to human are homo_sapiens_variation.txt.gz and humsavar.txt

[rashmi.bangalore123]

Thank you, this data was really helpful.

I also want to convert from ENSEMBL Transcript position (start and end coding sequence position) of the mutation to the corresponding position in the FASTA sequence of the Protein (UniProtKB).

Request you to please point me to how I can do this.

Thank you, Rashmi

[Elisabeth Gasteiger]

I'm afraid we do not currently have such a service at UniProt, but we are looking into it. There might be one in the future, and I suggest you follow the UniProt news (http://www.uniprot.org/news) or follow us on Twitter or Facebook.

[rashmi.bangalore123]

Thank you very much.