README.md

dop

A program for drawing dot plot by finding k-mer matches of two DNA sequences

Prerequisits

• Python (2.7.x)
• Gnuplot

Installation

$ git clone https://github.com/stomk/dop.git
$ cd dop
$ cd src && make

Getting started

Move into the example directory

$ cd example

and type

$ ../dop.py example.fasta

This will give example.fasta.20.png (20 indicates default k-mer size (20 bp)).

<img width=600 src="https://github.com/stomk/dop/blob/images/example/example.fasta.20.png", alt="default">

$ ../dop.py example.fasta -c

Will give a output file of the same name as above, with two-color dots (red dots represent forward matches and green dots reverse matches).

<img width=600 src="https://github.com/stomk/dop/blob/images/example/example.fasta.20c.png", alt="-c">

You can change the k-mer size with -k option.

$ ../dop.py example.fasta -k 40

<img width=600 src="https://github.com/stomk/dop/blob/images/example/example.fasta.40.png", alt="-k 40">

For more usage, type ../dop.py -h.