HOCOMOCO API (experimental; not stable)

HOCOMOCO allows for JSON APIs requests. Basically it's enough to add .json extension to an URL.

Get motif details

To get information about a motif MotifID, send a request hocomoco.autosome.ru/motif/{MotifID}.json

If you need to get PWM / PCM use hocomoco11.autosome.ru/motif/{MotifID}/pwm.json and hocomoco11.autosome.ru/motif/{MotifID}/pcm.json URLs.

hocomoco11.autosome.ru/motif/{MotifID}/thresholds.json gives you additionally a list of precalculated P-values for different PWM scores.

(deprecated) Alternatively you can add with_matrices=true and with_thresholds=true parameters to a general motif request: hocomoco.autosome.ru/motif/{MotifID}.json?with_matrices=true&with_thresholds=true

Get motif list

One can get a list of all motifs (only MotifIDs) in a collection by sending a request hocomoco11.autosome.ru/{species}/{arity}.json

species can be either human or mouse .

arity can be either mono for mononucleotide models or di for dinucleotide.

By default only core high-quality models are shown. Add ?full=true if you want D-quality models and alternative binding motifs to be listed.

Request hocomoco11.autosome.ru/{species}/{arity}.json?summary=true gives some additional information which can be useful to organize search through motif and gene names, TF family and subfamily names.

Motif search

Use the following request hocomoco11.autosome.ru/search.json?arity={arity}&species={species}&query={query} to search for a motif across `full_name` (MotifID), `motif_families` and `gene_names` fields. Any regexp can be given as a query.

hocomoco11.autosome.ru/search?family_id={TFClass id} returns a list of motifs from a TFClass group specified by TFClass id.