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MPG: Markov Process Generator of DNA sequences

Project description

Generates DNA sequences using a Markov Chain, learned from some reference sequence(s).

Many thanks to Ben Kaehler for a proof of concept and mathematical assistance.

Disclaimer: This is unstable software at the moment. Use with caution.


pip install cython numpy nose
pip install -U -e 'git+'


The script mpg should have been installed. This learns the transition probablitlies from sequences (in Fasta format) and generates random sequences from this Markov chain.

To learn transition probablities for a 5th-order Markov chain from the Arabidopsis genome and store them in a file (ath.yml):

mpg -k 5 -d ath.yml TAIR_10.fasta

To use these transition probablitlies to generate a sequence of 1000bp:

mpg -l 1000 -r ath.yml

To do the above operations at once:

mpg -l 1000 -k 5 TAIR_10.fasta

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