Markovian Sequence Generator
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.
pip3 install mpg
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 probabilities for a 5th-order Markov chain from the
Arabidopsis genome and store them in a file (
mpg -k 5 -d ath.h5 TAIR_10.fasta
To use these transition probablitlies to generate a sequence of 1000bp:
mpg -l 1000 -r ath.h5
To do the above operations at once:
mpg -l 1000 -k 5 TAIR_10.fasta