[ensembl-dev] Chromosome-HGNC mapping

[Manam, Monica (NIH/NCI) [F]]

Emily,

I shall try to use the below. Appreciate your help.

Thanks,
-- 
Monica Manam
CCRIFX BioInformatics CORE
NCI-NIH




On 7/19/13 4:06 AM, "Emily Pritchard" <emily at ebi.ac.uk> wrote:

>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_1D
>BSQL_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_1G
>ene.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
>
>
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