matrix-distrib
Computes the theoretical distribtuion of score probabilities of a given PSSM. It is not limited to a Bernoulli assumption and takes into account background models of any Markov order.
matrix-distrib [-i matrixfile] [-bgfile bgfile][-o outputfile] [-v]
The matrix format is specified with the option -matrix_format. Supported : tab,cb,consensus,gibbs,meme,assembly. Default : tab.
For a description of these format, see convert-matrix -h
The background model format is specified with the option -bg_format.Supported : oligo-analysis, MotifSampler, meme. Default is: oligo-analysis.
For a description of available format, see convert-backgound-model -h
The output is a tab-delimited file with the following columns:
P(W=w)
The scoring scheme is the weight (see matrix-scan -h for more details). We calculate in an exaustive way the probabilities that are associated to each score (weight) that can be obtained from a given PSSM.
For Bernoulli (Markov order 0) background models, the distribution of scores is computed with the algorithm described by Bailey (Bioinformatics, 1999).
For Markov background models with higher orders, we have extended this algorithm to take into account the dependencies between residues. For each iteration of the algorithm, weigths associated to all possible transitions are tagged with a prefix. Each residue weight is calculated according to the prefix tag. The prefix corresponds to a word of Markov order size that preceeds the position of the iteration.
This argument can be used iteratively to scan the sequence with multiple matrices.
Indicate a file containing a list of matrices to be used for scanning the region. This facilitates the scanning of a sequence with a library of matrices (e.g. all the matrices from RegulonDB, or TRANSFAC).
Format: the matrix list file is a text file. The first word of each row is suppose to indicate a file name. Any further information on the same row is ignored.
Background model file.
Supported formats: all the input formats supported by convert-background-model.