My last blog introduced WGDI software to draw a single species' dotplot, and participated in WGDI software (2): a single species * * * linear bitmap -dotplot. Next, I will show you two different species' dotplot. I chose Tripterygium wilfordii and grape genome. Tripterygium wilfordii and identification of cytochrome P450 involved in triptolide biosynthesis occurred once after Tripterygium wilfordii differentiated from grape.

First, the genome and gff3 files of Tripterygium wilfordii and Vitis vinifera are prepared, and six files, Vvin.len, Twi.len, Vvin.gff, Twi.gff, Twi.pep.fa and Vvin.pep.fa, are processed (see the previous blog for the processing method).

Then prepare the tripterygium wilfordii and grape protein comparison file Twi.Vvin.blastp

(1) Diagram 1 dotplot diagram drawn by WGDI, and Figure 2 is dotplot diagram drawn by quota software, both of which are based on the results of blastp.

(2) By comparison, we can find that the results of quota software display can basically be found in WGDI, which can give a conclusion consistent with the article (tripling has happened recently), and WGDI can display more information.

There are many softwares for drawing dotplot. I have used mummer, JCVI and quota, and each software has its own characteristics. Generally speaking, WGDI is the most user-friendly software, which can filter and draw the input file by simply modifying the configuration file, and can easily adjust the size of the picture.