RSAT Convert Matrix

What it does

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


Example with jaspar matrix:

>matrix1 matrix1
A [ 4 19 0 0 0 0 ]
C [ 16 0 20 0 0 0 ]
G [ 0 1 0 20 0 20 ]
T [ 0 0 0 0 20 0 ]

Results : tranfac matrix with output fields (consensus, parameters, frequencies and sites):

AC  m1
XX
ID  m1
XX
DE  m1 m1; from JASPAR
P0       A     C     G     T
1        4    16     0     0
2       19     0     1     0
3        0    20     0     0
4        0     0    20     0
5        0     0     0    20
6        0     0    20     0
XX
CC  program: jaspar
CC  matrix.nb: 1
CC  min.prior: 0.25
CC  alphabet.size: 4
CC  max.bits: 2
CC  total.information: 6.56407409450406
CC  information.per.column: 1.09401234908401
CC  max.possible.info.per.col: 1.38629436111989
CC  consensus.strict: CACGTG
CC  consensus.strict.rc: CACGTG
CC  consensus.IUPAC: CACGTG
CC  consensus.IUPAC.rc: CACGTG
CC  consensus.regexp: CACGTG
CC  consensus.regexp.rc: CACGTG
CC  residues.content.crude.freq: a:0.1917|c:0.3000|g:0.3417|t:0.1667
CC  G+C.content.crude.freq: 0.641666666666667
CC  residues.content.corrected.freq: a:0.1944|c:0.2976|g:0.3373|t:0.1706
CC  G+C.content.corrected.freq: 0.634920634920635
XX
//

Citation

For the underlying tool, please cite Thomas-Chollier, M., Defrance, M., Medina-Rivera, A., Sand, O., Herrmann, C., Thieffry, D. and van Helden, J. (2011). RSAT 2011: regulatory sequence analysis tools. Nucleic Acids Research doi: 10.1093/nar/gkr377.