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Syntenic Viewer

Download & Installation

Download syntenic viewer module from github

cd /var/www/html/youSiteFolder/sites/all/modules/
git clone https://github.com/tripal/tripal_synview

Install syntenic viewer through "Administration of Modules" of Drupal.

Or install syntenic viewer using command:

drush pm-enable tripal_synview

Detection of synteny blocks and collinearity genes

Please follow the documentation of MCScanX

Load MCScanX results

1. convert MCScanX results

Imagine that we have two genomes (named aa and bb) that need to be analyzed. We already generated below files required by MCScanX in previous step:

aa_bb.gff
aa_bb.blast

And we also have the output of MCScanX which contains collinearity genes.

aa_bb.collinearity

For most genomes, the chromosome usually named as chr1, chr2, chr3 ... The aa and bb may have same name of chromosomes. So we need another file aa_bb.chr which contains new and old names of chromosomes. Format of aa_bb.chr:

chr1    aa1
chr2    aa2
...	    ...
chr1    bb1
chr2    bb2
...     ...

We could retirve the block information between aa and bb from the list of collinearity genes

perl syntenyTool.pl -t mcscanx_block -c aa_bb.chr aa_bb.collinearity aa_bb.gff > aa_bb.block

Next, please find the organism_id for the genome aa and bb in chado database. In this exmaple, the organism_id is 1 and 2 for genome aa and bb, separately. We generate the file that could be load in to chado using below command:

perl syntenyTool.pl -t mcscanx_tripal -a aa -b bb -c 1 -d 2 aa_bb.chr aa_bb.gff aa_bb.collinearity aa_bb.block > aa_bb.block.tripal.txt

2. Load list of collinearity genes

Login tripal with adaministrator, then:

add content -> synteny file

Please input a human-readable name for synteny file, such as:

"synteny analysis for aa and bb".

Please select corresponding genomes for aa and bb.

Next, File name and location (Full Path)

home/web/synteny/aa_bb_block.tripal.txt

Finally, do not forget check option for "Insert/update synteny files to chado database" and run tripal jobs to insert blocks and collinearity genes to datbase.