https://github.com/tripal/tripal_synview
synteny viewer
https://github.com/tripal/tripal_synview
Last synced: about 1 month ago
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synteny viewer
- Host: GitHub
- URL: https://github.com/tripal/tripal_synview
- Owner: tripal
- Created: 2017-02-27T19:22:24.000Z (about 8 years ago)
- Default Branch: master
- Last Pushed: 2018-09-05T03:05:58.000Z (over 6 years ago)
- Last Synced: 2025-03-21T06:33:25.887Z (2 months ago)
- Language: PHP
- Size: 138 KB
- Stars: 6
- Watchers: 3
- Forks: 3
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
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README
# Syntenic Viewer
## Download & Installation
Download syntenic viewer module from [github](https://github.com/tripal/tripal_synview)
```
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](http://chibba.pgml.uga.edu/mcscan2/) 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.