Ensembl Database Fetch Sequence Problem

Question

[roger770507]

hello

i just download the mySQL data from Ensembl and successful construct the database (homo spaien core 73)

but my problem is if i had a ENST ID (ex: ENST00000575820)

how do i fetch the sequence via the database?

i already read the manual but haven't found any info how to do it.

plz help me , thanks!

Answer 1

[Emily]

Hi Roger

MySQL queries are not really ideal for extracting sequences. Because of the way the tables are structured you end up having to extract regions then pull out various segments for each of the exons, then pull them together, and can be particularly complicated if your transcript(s) of interest is/are reverse stranded.

A much better way to get transcript sequences is via the Perl API. There's an online course on using the API here. Then you can fetch a transcript by its ID using the TranscriptAdaptor and get its sequence, and the API will do all the complicated processing for you.

Alternatively, you can use the REST API, which has a very simple method for getting transcript sequences.

Hope this helps

Emily

[roger770507]

Thanks! Emily! i just wondering that can i get the name (ex: AP005530.1-002=ENST00000575820) via the REST API too? like this http://beta.rest.ensembl.org/documentation/info/feature_id ?

[Emily]

This should do it.