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Motif database of choice

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
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updated by Zcat2010 • Zcat2010 • written by rbronste rbronste

Jaspar and TRANSFAC are used widely I guess..

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written by Prakash Prakash

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.

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written by Zcat2010 • Zcat2010

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.

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written by jared.andrews07 jared.andrews07

1 answer

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).

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written by jared.andrews07 jared.andrews07

Yes Ive tried a number of them, currently using RSAT but have gone through HOMER (slightly outdated) and MEME.

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written by rbronste rbronste

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