HOCOMOCO allows for JSON APIs requests. Basically it's enough to add .json extension to an URL.
To get information about a motif
MotifID,
send a request
https://hocomoco11.autosome.org/motif/{MotifID}.json
If you need to get PWM / PCM use
https://hocomoco11.autosome.org/motif/{MotifID}/pwm.json
and
https://hocomoco11.autosome.org/motif/{MotifID}/pcm.json
URLs.
https://hocomoco11.autosome.org/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:
https://hocomoco11.autosome.org/motif/{MotifID}.json?with_matrices=true&with_thresholds=true
One can get a list of all motifs (only MotifIDs) in a collection by sending a request
https://hocomoco11.autosome.org/{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
https://hocomoco11.autosome.org/{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.
Use the following request
https://hocomoco11.autosome.org/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.
Add
&summary=true
or
&detailed=true
if you want detailed information.
https://hocomoco11.autosome.org/search?family_id={TFClass id}
returns a list of motifs from a TFClass group specified by TFClass id.