Loading genome files
We can install a genome to GenIE-Sys using either Graphical User Interface (GUI) or Command Line Interface (CLI).
Once you have placed all the required files into the data folder according to the previous section (Input files). You will be able to see the annotation tab similar to the following screenshot.
If you miss some of the files described in the previous section, you will be able to see the error message similar to the following screenshot.
Please make sure to place the correct files into the data folder. Once you have placed all required files, now it's time to parse them into the suitable formats right before loading into the database. Please follow the order in the Annotation tab, first load data into the database and then create BLAST indices using Generate FASTA indices link.
If you have expression data please go to the next tab otherwise please log out from the site and see all your changes are displayed on the GeneList, BLAST and gene information pages.
Creating a new database using CMD
Due to the increasing number of species in PlantGenIE we use a standard naming convention to easily identify and maintain the databases. For example: [website name]_[species name]_[version number]
Log into the MySQL server and create a database.
You can download the empty database here. Then load the database into the newly created database using the following commands.
Log into the MySQL server to create user and grant permissions.
Create MySQL user
User permissions
newuser, newpassword and new_database should be included in the plugins/settings.php similar to following example.
Download
Let’s assume we need to integrate Populus tremula v2.0 genome into GenIE-System. First, we need to download the required files. The latest version of the GFF3 and FASTA files are available on PlantGenIE FTP.
Parse genome
Now we need to parse GFF3 and FASTA files into required formats. There are two primary tables(transcript_info and gene_info) in the database.
Create a database
Now we need to create a database. To do this, you need a MySQL username and password. If you use the MAMP installation default username and password would be root.
Loading primary tables
Now we need to load above two files(gene_info.txt and transcript_info.txt) into the newly created database. There is a script(load_data.sh) to do this. We can download the script and enter the correct username, password and database information to DB_USER, DB_PASS and DB parameters respectively.
Run following commands to load gene_info.txt and transcript_info.txt into respective tables.
Now we need to update the gene_i parameter in transcript_info table. There is a script(update_gene_i.sh) in the scripts directory, we just need to enter the correct username, password and database information to DB_USER, DB_PASS and DB parameters respectively as we did in previous step.
Let’s run the following command to update gene_i in transcript_info table.
If above script takes time please try following command on MySQL. This will update the gene_i column in transcript_info table.
Run following command to execute the above script(update_gene_i_dev.sh)
Great! We have loaded transcript and gene infortmation properly into the database. Now can we load additional information. For example; description to the transcript_info table.
Here is the script to load description into transcript_info column.
We just need to run the script to load description into transcript_info table.
Loading secondary tables
Following are the tables available with GenIE-Sys default database. However, it is easy to add more tables depending on the user demands. Secondary table conatins annotation related to the primary tables.
As you see the annotation are based on transcript IDs. Therefore, Following script can be used to load secondary table into transcript_go table. Then update transcript_i column using another script as described below.
Then update the gene_i or transcript_i depending on the primary usint of the annotation dataset using following script.
Let’s run following command to fill the transcript_i or gene_i column.
Similalrly when we have annotation based on gene IDs, we have to fill gene_annotation tables.
You may also load additional annotation as secondary tables to the GenIE-Sys database. If there is a transcript-based annotation, please use the following script to create a corresponding table (please replace annotation with the name of the annotation).
If there is a gene-based annotation, please use the following script to create a corresponding table (please replace annotation with the name of the annotation).
Finally you may need to add the new annotation into /plugins/genelist/genelist/service/config.php to make it searchable in the GeneSearch tool.
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