How to do Genome Collinearity Analysis by MCscan

This article mainly introduces how MCscan does genome collinearity analysis. It is very detailed and has certain reference value. Friends who are interested must finish reading it.

Collinear analysis of multi-genomic gene level

In the collinearity analysis of multi-gene collinearity and local gene level and genomic collinearity analysis, this paper talks about how MCscan does genome collinearity analysis, and here we talk about the collinearity analysis of multi-genome gene level.

The method is to do collinear analysis of pairwise genomes. Or take peaches, grapes and cocoa as examples, as follows:

$python-m jcvi.compara.synteny mcscan grape.bed grape.peach.lifted.anchors-- iter=1-o grape.peach.i1.blocks$ python-m jcvi.compara.synteny mcscan grape.bed grape.cacao.lifted.anchors-- iter=1-o grape.cacao.i1.blocks$ python-m jcvi.formats.base join grape.peach.i1.blocks grape.cacao.i1.blocks-- noheader | cut-F1 2Jing 4 Jing 6 > grape.blocks

Select the areas of interest for display, and here show the first 50 columns:

$head-50 grape.blocks > blocks2

The blocks2 file format is as follows:

GSVIVT01012261001. .GSVIVT01012259001 ppa005716m .GSVIVT01012258001. .GSVIVT01012257001 ppa002846m .GSVIVT01012255001 ppa000919m Thecc1EG011472t1GSVIVT01012253001 ppa010733m Thecc1EG011473t1GSVIVT01012252001 ppa015194m Thecc1EG011474t1

The configuration file is as follows:

# x, y, rotation, ha, va, color, ratio, label0.5, 0.6, 0, center, top, 1, grape Chr10.3, 0.4, 0, center, bottom,. 5, peach scaffold_10.7, 0.4, 0, center, bottom,. 5, cacao scaffold_2# edgese, 0, 1e, 0, 2

Run the drawing:

$cat grape.bed peach.bed cacao.bed > grape_peach_cacao.bed $python-m jcvi.graphics.synteny blocks2 grape_peach_cacao.bed blocks2.layout and above are all the contents of the article "how to do Genomic Collinearity Analysis by MCscan". Thank you for reading! Hope to share the content to help you, more related knowledge, welcome to follow the industry information channel!