We, Russian scientists of the autosome team, are depressed by the dire events caused by Russian military actions in Ukraine.
We express our condolences to all affected people and sincerely hope for a prompt transition to peace.
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HOCOMOCO v10 is outdated.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

Contacts
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
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
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

See also:

Curation log
Retracted models