HOCOMOCO-v10 Downloads - HOmo sapiens COmprehensive MOdel COllection

Downloads (HOCOMOCO-10)

Attention!

HOCOMOCO v10 is outdated. Please use the latest HOCOMOCO release.

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/zip (~200Mb).
ChIP-Seq peaks used for benchmarking, MultiFASTA/zip (~200Mb).

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: expansion and enhancement of the collection of transcription factor binding sites models

Ivan V. Kulakovskiy; Ilya E. Vorontsov; Ivan S. Yevshin; Anastasiia V. Soboleva; Artem S. Kasianov; Haitham Ashoor; Wail Ba-alawi; Vladimir B. Bajic; Yulia A. Medvedeva; Fedor A. Kolpakov; Vsevolod J. Makeev

Nucl. Acids Res. (04 January 2016) 44 (D1): D116-D125.

doi: 10.1093/nar/gkv1249

TFBS models (Technical notes)

		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	H10_HUMAN_mono_jaspar_format.txt		H10_MOUSE_mono_jaspar_format.txt
	MEME	H10_HUMAN_mono_meme_format.meme		H10_MOUSE_mono_meme_format.meme
	TRANSFAC	H10_HUMAN_mono_transfac_format.txt		H10_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

Tools

Sequence data

TFBS models (Technical notes)

See also: