RSAT - convert-matrix

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


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

Prokaryotes

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

Multi-organisms

RSAT non-redundant insects+plants+vertebrates - [2889 motifs] (2017) - [local copy]
footprintDB all - [11066 motifs] (2018-06) - [local copy]
JASPAR core nonredundant all - [1404 motifs] (2018) - [local copy]
JASPAR core redundant all - [1564 motifs] (2018) - [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

    Organism-specific

      Genomes in the RSAT Prokaryotes server were recently re-installed. Genome names now follow the NCBI standard to easily identify assemblies, if you cannot find your genome please check this naming list to find the correct ID: Genome IDs list

      Organism 
      [List of organisms] not seeing your favorite organism in the list ? Contact us to have it installed
      Sequence type  

    Estimate from input matrix

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



Output format 

Output fields 
 counts
 frequencies
 weights
 info
 header
 margins
 consensus
 parameters
 profile
 comments
 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'.

Output  

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