[ensembl-dev] Chromosome-HGNC mapping

[Emily Pritchard]

Hi Monica

Yes, you can do that.

Use fetch_by_external_id in the gene_adaptor module to get genes from 
our database using HGNC or RefSeq IDs:
http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1DBSQL_1_1GeneAdaptor.html#a940d6dc7e9273ad373a23eb563a455e6

Then you can use commands from the Gene module to get various bits of 
information:
http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1Gene.html

You may wish to use seq_region_name, seq_region_start and seq_region_end 
to get coordinates, while get_all_Exons and get_all_Transcripts will 
give you exons and transcripts respectively.

Hope this helps

Emily
Ensembl Outreach


On 18/07/2013 19:30, Manam, Monica (NIH/NCI) [F] wrote:
> Hello Team,
>
> I have a question regarding the API which gives the Gene & it's attributes mapping.
> For a given HGNC/RefSeq Id , can we get the chromosome name & its start & end , transcript , exon , & gene information?
>
> I know the API under "Genes, Transcripts, and Exons" to get the gene data, & it takes the chromosome number, start & end as input.
>
> Thanks ,
> --
> Monica Manam
> CCRIFX BioInformatics CORE
> NCI-NIH
>
>
>
>
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-- 
Dr Emily Pritchard
Ensembl Outreach Officer

EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge
CB10 1SD
UK