RSAT - footprint-scan

Pipeline for footprint-scan.


Conceptionc, implementationi and testingt: Jacques van Heldencit , Alejandra Medina-Riveracit

Matrix Matrix (or matrices)        Format 


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Vertebrates

Hocomoco (Human TFs) - [771 motifs] (2017-10) - [local copy]
Hocomoco (Mouse TFs) - [531 motifs] (2017-10) - [local copy]
Homer (Human TF motifs) - [332 motifs] (2016-07) - [local copy]
Jolma_2013 (Human TFs) - [818 motifs] (2015-11) - [local copy]
Jolma_2013 (Human TFs dimers) - [664 motifs] (2016-05) - [local copy]
RSAT non-redundant vertebrates - [2233 motifs] (2017) - [local copy]
cisBP human - [1832 motifs] (2014-10_v0.9) - [local copy]
cisBP mouse - [1715 motifs] (2014-10_v0.9) - [local copy]
Epigram (Human Histone marks related motifs) - [589 motifs] (2016-06) - [local copy]
hPDI (Human TFs identified by protein microarray assays) - [437 motifs] (2016-06) - [local copy]
JASPAR core nonredundant vertebrates - [579 motifs] (2018) - [local copy]

Non-vertebrate Metazoa

Drosophila DMMPMM - [41 motifs] (2010_11) - [local copy]
DrosophilaTFs - [61 motifs] (2015-11) - [local copy]
Drosophila IDMMPMM - [39 motifs] (2010_11) - [local copy]
RSAT non-redundant insects - [350 motifs] (2017) - [local copy]
cisBP c_elegans - [1499 motifs] (2015-05_v1.02) - [local copy]
cisBP drosophila - [1427 motifs] (2014-10_v0.9) - [local copy]
footprintDB-metazoa [only metazoa DNA motifs] - [7296 motifs] (2017-12) - [local copy]
JASPAR core nonredundant insects - [133 motifs] (2018) - [local copy]
JASPAR core nonredundant nematodes - [26 motifs] (2018) - [local copy]
JASPAR core nonredundant urochordates - [1 motifs] (2018) - [local copy]

Plants

ArabidopsisPBM (A thaliana) - [108 motifs] (2015-11) - [local copy]
Athamap (A thaliana) - [84 motifs] (2015-11) - [local copy]
RSAT non-redundant plants - [306 motifs] (2017) - [local copy]
Cistrome (A thaliana motifs detected by DAP-seq) - [862 motifs] (2016-06) - [local copy]
footprintDB-plants [only plant DNA motifs] - [2028 motifs] (2017-12) - [local copy]
JASPAR core nonredundant plants - [489 motifs] (2018) - [local copy]

Fungi

Yeastract s_cerevisiae - [732 motifs] (20130918) - [local copy]
cisBP s_cerevisiae - [776 motifs] (2015-06_v1.02) - [local copy]
JASPAR core nonredundant fungi - [176 motifs] (2018) - [local copy]

Prokaryotes

DBTBS (Bacillus Subtilis) - [88 motifs] (2015-11) - [local copy]
RegulonDB prokaryotes - [93 motifs] (2015_08) - [local copy]

Multi-organisms

footprintDB all - [11763 motifs] (2017-12) - [local copy]
JASPAR core nonredundant all - [1404 motifs] (2018) - [local copy]

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Pseudo-counts distributed in an equiprobable waydistributed proportionally to residues priors


Background model estimation method

Pseudo-frequencies


Output