Motif database of choice
1
0
Entering edit mode
7.1 years ago
rbronste ▴ 420

Wondering what people working with mouse and human samples prefer, since there are so many choices from Jaspar to cisBP - interested in what is standard out there, especially for mouse? Thanks.

motif RSAT ChIP-Seq • 3.0k views
ADD COMMENT
0
Entering edit mode

Jaspar and TRANSFAC are used widely I guess..

ADD REPLY
0
Entering edit mode

I'm also interested in this question for humans. CIS-BP aggregates PWMs from many sources, but is it better than HOCOMOCO? Haven't been able to find a paper or post that provides a direct comparison of the two.

ADD REPLY
0
Entering edit mode

CIS-BP hasn't been updated since 2015, so it has a lot of 'inferred' motifs for TFs that HOCOMOCO has direct evidence for instead, as it's continually updated. I would use HOCOMOCO or JASPAR over CIS-BP personally, though calling them 'better' is somewhat subjective.

ADD REPLY
2
Entering edit mode
7.1 years ago

It's really up to you, though there are many of them, and there's a lot of overlap between them in terms of datasets they use to define their motifs.

JASPAR and TRANSFAC have already been mentioned, but ENCODE also has their own list. There is also HOCOMOCO, which is one of my personal favorites.

Several programs also have their own lists or collections of databases - see HOMER and the MEME suite (which has literally dozens of databases, probably the best compendium around).

ADD COMMENT
0
Entering edit mode

Yes Ive tried a number of them, currently using RSAT but have gone through HOMER (slightly outdated) and MEME.

ADD REPLY

Login before adding your answer.

Traffic: 1322 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6