Connect to JASPAR database with biopython

Question

[themantalope]

Hi All,

I've done an analysis where I've identified DNA motifs and mapped them to known TF-binding motifs within the JASPAR database. Now, I need to get some of the meta-data associated with the JASPAR id of the matched motif. According to biopython I should be able to connect to a JASPAR database and query it through the biopython API. However, my understanding is that using this method it is up to the user to know what URL they need to have in order to connect to the database. Is there a public URL through which one can access the JASPAR database? The documentation on the JASPAR webpage doesn't give any specifics.

Answer 1

[asntech]

Hi, JASPAR doesn't provide any public connection to the mysql server, but it provides the whole database as mysqldump. You can use it to setup a local mysql instance and query it using biopython.

JASPAR now provide a REST API to get data from the latest release (2018) and also older releases of JASPAR. Here is the API http://jaspar.genereg.net/api/ and here is an interactive documentation http://jaspar.genereg.net/api/v1/docs

P.S. Although, it is a late answer, but I'm posting this if someone else have similar questions.