RSAT - footprint-scan

Pipeline for footprint-scan.


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

Matrix Matrix (or matrices)        Format 

Or select a file to upload


Or Dynamic selection of motifs from the available collections
(select the collection and a dropdown menu will appear to select motifs)


View matrix descriptions & download full collections

Fungi

Yeastract s_cerevisiae - [732 motifs] (20130918) - [local copy]
cisBP s_cerevisiae - [776 motifs] (2015-06_v1.02) - [local copy]
cisBP Saccharomyces_cerevisiae - [1288 motifs] (2019-06_v2.00) - [local copy]
JASPAR core nonredundant fungi - [183 motifs] (2020) - [local copy]
JASPAR core redundant fungi - [184 motifs] (2020) - [local copy]

Multi-organisms

RSAT non-redundant insects+plants+vertebrates - [2889 motifs] (2017) - [local copy]
footprintDB all - [11145 motifs] (2019-07) - [local copy]
JASPAR core nonredundant all - [1646 motifs] (2020) - [local copy]
JASPAR core redundant all - [1964 motifs] (2020) - [local copy]
JASPAR unvalidated - [337 motifs] (2020) - [local copy]

RNA binding

ATtRACT - [1322 motifs] (2017) - [local copy]
CISBP-RNA - [11897 motifs] (2017) - [local copy]
RBPDB - [71 motifs] (2017) - [local copy]

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


Background model estimation method

Pseudo-frequencies


Output