[ensembl-dev] Accessing sequence information without using the Perl API

[Premanand Achuthan]

Hello Felix

You could use the ensembl REST server (http://rest.ensembl.org/)

To retrieve the list of available species and genome builds, use the 
info/species endpoint:
http://rest.ensembl.org/info/species?content-type=application/json

To retrieve the sequence information, use the sequence endpoint:

http://rest.ensembl.org/documentation/info/sequence_region_post (Request 
multiple types of sequence by a list of regions)

http://rest.ensembl.org/documentation/info/sequence_region (Returns the 
genomic sequence of the specified region of the given species)

Please be aware that there is a rate limit (15 requests per second)

More info in User Guide:
https://github.com/Ensembl/ensembl-rest/wiki
https://github.com/Ensembl/ensembl-rest/wiki/Rate-Limits

Hope it helps,

Best Regards
Prem

On 03/01/2018 20:24, Felix Krueger wrote:
>
> Dear all,
>
> I am looking to use the Ensembl API to retrieve lists of available 
> species and genome builds, as well as potentially large numbers of 
> sequence information for sets of coordinates of various genomes. For 
> this Java-based project we cannot use the Perl API, but could 
> potentially use the REST or direct MySQL access. Would anyone be able 
> to give me a pointer to what is likely the best way for me going forward?
>
> Many thanks and a Happy New Year!
>
> Kind regards,
>
> Felix
>
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