Retrieving Information From Ensembl Without Knowing The Speices

Question

[sarahmanderni]

Hi,

I have a protein ID list from different species and I need to retrieve some other attributes for them. Biomart needs to know the species name when querying. Is there any other solution to get the attributes without specifying the species name? Thanks

Answer 1

[Emily]

Are your IDs in the form ENS[three letters]P###########? If so, you can determine what species they are by the three letters. There's a list of three letter codes here.

[Prakki Rama]

@Emily_Ensembl But, i think still we cannot download all the sequences from different species at one go given the ID's. We have to download specieswise is it?

[Emily]

Not through BioMart. BioMart will only do one species at a time. If you have a mixture, you might be looking at the REST API instead. This sequence endpoint will allow you to put in your ID and get the sequence out, without needing to specify the species as well. You can then use your programming language of choice to go through your list, constructing the query for each one and parsing the output. There are usage restrictions on our REST API so you may wish to put in place some time delays in your script.

[Prakki Rama]

Thanks. It is clear now.