Tools

MoLoTool - web interface for motif finding.
SPRY-SARUS tool for motif finding (Java): jar, readme
MACRO-APE tool for motif comparison, P-value and threshold estimation: jar, manual, website
PERFECTOS-APE tool for functional annotation of sequence variants overlappint TFBS: jar, manual, website

Sequence data

ChIP-Seq peaks used for motif discovery, MultiFASTA/tgz (~490Mb).
ChIP-Seq peaks used for benchmarking, MultiFASTA/tgz (~490Mb).

Collection preparation

Motif quality assessment scripts, github.

Contacts

Technical questions and suggestions should be addressed to Ilya Vorontsov and Ivan Kulakovskiy.
General questions should be addressed to Ivan Kulakovskiy, Yulia Medvedeva or Vsevolod Makeev.

Citation:

HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis

Ivan V. Kulakovskiy; Ilya E. Vorontsov; Ivan S. Yevshin; Ruslan N. Sharipov; Alla D. Fedorova; Eugene I. Rumynskiy; Yulia A. Medvedeva; Arturo Magana-Mora; Vladimir B. Bajic; Dmitry A. Papatsenko; Fedor A. Kolpakov; Vsevolod J. Makeev

Nucl. Acids Res., Database issue, gkx1106 (11 November 2017)

doi: 10.1093/nar/gkx1106

License: HOCOMOCO motif collection is distributed under WTFPL. If you prefer more standard licenses, feel free to treat WTFPL as CC-BY.

TFBS models (Technical notes)

CORE COLLECTION: primary binding models of ABC quality

		Human		Mouse
		Mononucleotide	Dinucleotide	Mononucleotide	Dinucleotide
Complete model annotation (including gene id mapping)		annotation_HUMAN_mono.tsv	annotation_HUMAN_di.tsv	annotation_MOUSE_mono.tsv	annotation_MOUSE_di.tsv
PWM	One file per matrix	pwm_HUMAN_mono.tar.gz	pwm_HUMAN_di.tar.gz	pwm_MOUSE_mono.tar.gz	pwm_MOUSE_di.tar.gz
PWM	Flat file	pwms_HUMAN_mono.txt	pwms_HUMAN_di.txt	pwms_MOUSE_mono.txt	pwms_MOUSE_di.txt
PCM	One file per matrix	pcm_HUMAN_mono.tar.gz	pcm_HUMAN_di.tar.gz	pcm_MOUSE_mono.tar.gz	pcm_MOUSE_di.tar.gz
PCM	Flat file	pcms_HUMAN_mono.txt	pcms_HUMAN_di.txt	pcms_MOUSE_mono.txt	pcms_MOUSE_di.txt
Alignments		words_HUMAN_mono.tar.gz	words_HUMAN_di.tar.gz	words_MOUSE_mono.tar.gz	words_MOUSE_di.tar.gz
Standard thresholds		standard_thresholds_HUMAN_mono.txt	standard_thresholds_HUMAN_di.txt	standard_thresholds_MOUSE_mono.txt	standard_thresholds_MOUSE_di.txt
Threshold to P-value map		thresholds_HUMAN_mono.tar.gz	thresholds_HUMAN_di.tar.gz	thresholds_MOUSE_mono.tar.gz	thresholds_MOUSE_di.tar.gz
Sequence LOGOs		logo_HUMAN_mono.tar.gz	logo_HUMAN_di.tar.gz	logo_MOUSE_mono.tar.gz	logo_MOUSE_di.tar.gz
Matrices in other formats	JASPAR	H11_HUMAN_mono_jaspar_format.txt		H11_MOUSE_mono_jaspar_format.txt
	MEME	H11_HUMAN_mono_meme_format.meme		H11_MOUSE_mono_meme_format.meme
	TRANSFAC	H11_HUMAN_mono_transfac_format.txt		H11_MOUSE_mono_transfac_format.txt
	HOMER	P-value 0.001 P-value 0.0005 P-value 0.0001		P-value 0.001 P-value 0.0005 P-value 0.0001

FULL COLLECTION: primary and alternative binding models^*

*Available dinucleotide models are fully represented by the CORE dinucleotide collection (see above).

		Human mononucleotide	Mouse mononucleotide
Complete model annotation (including gene id mapping)		annotation_HUMAN_mono.tsv	annotation_MOUSE_mono.tsv
PWM	One file per matrix	pwm_HUMAN_mono.tar.gz	pwm_MOUSE_mono.tar.gz
PWM	Flat file	pwms_HUMAN_mono.txt	pwms_MOUSE_mono.txt
PCM	One file per matrix	pcm_HUMAN_mono.tar.gz	pcm_MOUSE_mono.tar.gz
PCM	Flat file	pcms_HUMAN_mono.txt	pcms_MOUSE_mono.txt
Alignments		words_HUMAN_mono.tar.gz	words_MOUSE_mono.tar.gz
Standard thresholds		standard_thresholds_HUMAN_mono.txt	standard_thresholds_MOUSE_mono.txt
Threshold to P-value map		thresholds_HUMAN_mono.tar.gz	thresholds_MOUSE_mono.tar.gz
Sequence LOGOs		logo_HUMAN_mono.tar.gz	logo_MOUSE_mono.tar.gz
Matrices in other formats	JASPAR	H11_HUMAN_mono_jaspar_format.txt	H11_MOUSE_mono_jaspar_format.txt
	MEME	H11_HUMAN_mono_meme_format.meme	H11_MOUSE_mono_meme_format.meme
	TRANSFAC	H11_HUMAN_mono_transfac_format.txt	H11_MOUSE_mono_transfac_format.txt
	HOMER	P-value 0.001 P-value 0.0005 P-value 0.0001	P-value 0.001 P-value 0.0005 P-value 0.0001