Genome Analyzer MCScanX collinearity

 Software Description

MCScan X-toolset for MCScan adjustment algorithm, for detecting and collinearity with the linear region, but also increases the visual and downstream analysis. . There are three core MCscanX tool, and tool 12 downstream analysis.

Software Installation

 Enter the official website http://chibba.pgml.uga.edu/mcscan2/#tm , download and install

1 unzip MCscanX.zip
2 cd MCScanX
3 make

 

 Software

•  Required documents

　　　　 Gff or two files, a plurality of species of protein sequences (** The software can do up to five species collinearity )

• The first step: to build an index, a ratio of blastp

note! Here is a look at and within vv two genomic organization and co-linearity between the groups, because I wanted knowing that collinearity within and between species and species, so before the blast to at and vv genome facat together, not only do the database, and do the query, if want to know collinearity among the group, then became taking a genome database, do another query

note!  If a plurality of gene transcripts, only select the first annotation

1 ## 合并
2 cat at.fa vv.fa >>all.fa
3 
4 ## 建库
5 makeblastdb -in all.fa -dbtype prot -out index/all -parse_seqids
6 
7 ## 比对
8 blastp -query all.fa -db index/all -out all.blast -evalue 1e-5 -num_threads 10 -outfmt 6 -num_alignments 5

• Step Two: Build gff file 

MCscanX requirements gff files and standard gff file is not the same, it is only four, which "sp #" means that you use the sp 2 letters represent the species, # indicates what chromosomes. The "gene" is a gene will have the name of your protein sequence

Note: all.gff, all.blastp prefix as needed, and at the same folder

1 sp# gene    starting_position  ending_position

 According gff3 species file using awk quickly get gff file MCscanX requirements

• The third step: MCScanX find collinearity block

1 MCScanX ./all

 

•  The results file

 The output file is divided into two:

　　　　　　　　The first is at_rice.collinearity, recorded collinearity block (collinear blocks)

 

 

 

 

Tool genome collinearity instructions MCScanX

Tool genome collinearity instructions MCScanX