Generate Background Sequences Using Markov Model

Cited from GimmeMotifs documentation

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generate_background_sequences.py

Generate random sequences according to one of two methods: random or matched_genomic. With the argument type set to random, and an input file in FASTA format, this script will generate sequences with the same dinucleotide distribution as the input sequences according to a 1st order Markov model trained on the input sequences. The -n options is set to 10 by default. The length distribution of the sequences in the output file will be similar as the inputfile. The Markov model can be changed with option -m. If the type is specified as matched_genomic the inputfile needs to be in BED format, and the script will select genomic regions with a similar distribution relative to the transcription start of genes as the input file. Make sure to select the correct genome. The length of the sequences in the output file will be set to the median of the features in the input file.
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What Is The Appropriate Order For A Background Model In Motif Searches?

Implemention of fasta-get-markov on GUI