RSAT - convert-matrix

Convert different formats of position-specific scoring matrices (PSSM), and calculate statistical parameters and generate logos.

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


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]


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


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      Sequence type  

    Estimate from input matrix

Note: Only Bernoulli models are supported. Higher-order Markov models are converted into Markov 0 (Bernoulli).

Output format 

Output fields 
 logo (using Weblogo)    (options:      )

score decimals
Compute reverse complement
Multiply counts (convert frequency matrices into count matrices)
Insert columns           Left side          Right side

Permutations For random controls. Note: this option only returns 'counts'.