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GO FEAT: a rapid web-based functional annotation tool for genomic and transcriptomic data

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# GO FEAT

[GO FEAT](http://computationalbiology.ufpa.br/gofeat/) is a free, online, user friendly platform for functional annotation and enrichment of genomic and transcriptomic data based on homology search analysis. GO FEAT overcomes the limitations of current tools by allowing users to generate reports, tables, GO charts and graphs that help the user with downstream analysis of data. In addition, GO FEAT allow users to export the results with different output formats.

### Requisites
You will need to have a webserver already configured using Apache, PHP and MySQL. The same principle is valid if you want to use DIAMOND.

### Instalation

In order to run GO FEAT in your local web server, you need to perform these steps:
1. Create the "gofeat" directory in your web server's root directory and clone GO FEAT project into it:
```
cd gofeat
git clone https://github.com/fabriciopa/gofeat
```

2. Create a MYSQL database and import the [gofeat.sql](http://computationalbiology.ufpa.br/gofeat/gofeat.sql.gz) file to it.

3. Configure the 'gofeat/application/configs/application.ini' file for the database (lines 13-16), your email for UNIPROT usage (line 21) and DIAMOND (lines 24-35) usage;

Database parameters you need to change:
```
resources.multidb.name1.dbname = YOUR_DATABASE_NAME
resources.multidb.name1.username = YOUR_DATABASE_USERNAME
resources.multidb.name1.password = "YOUR_DATABASE_PASSWORD"
resources.multidb.name1.host = "YOUR_DATABASE_SERVER"
```
UNIPROT parameters you need to change:
```
diamond.emailEbi = "YOUR_EMAIL [REQUIRED]"
```
DIAMOND parameters you need to change:
```
diamond.useDiamond = "false"
;number of sequences before start using DIAMOND
diamond.nSeqs = "999999999"
diamond.remoteDiamond = "true (in case you want to run the diamond in another server)"
diamond.nCore =  "number_of_cores_for_diamond (integer)"
diamond.remoteHost = "remote_ip_diamond_server"
diamond.remotePort = "remote_port_diamond_server"
diamond.remoteUser = "remote_user_diamond_server"
diamond.remotePwd = "remote_password_diamond_server"
diamond.workDir = "diamond_work_directory (remote or local)"
diamond.uniprotkb = "diamond_uniprotkb_database_directory (remote or local)"
diamond.diamondbin = "path_to_your_diamond"
```
3. Start the bots to check if any new sequence needs to be annotated:
```
nohup wget -O bot http://YOUR_WEB_SERVER/gofeat/index/botblast &
```
If you are using DIAMOND, also start the DIAMOND bot:
```
nohup wget -O bot http://YOUR_WEB_SERVER/gofeat/index/botdiamond &
```
By default, all tests published in our paper are registered for the user:
Email: admin@admin.com
Password: 123456

## Authors
* **Fabricio Araujo** - *Universidade Federal do Pará, Instituto de Ciências Biológicas* - [GOFEAT](http://computationalbiology.ufpa.br/gofeat/)
* **Debmalya Barh** - *Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology´*
* **Artur Silva** - *Universidade Federal do Pará, Instituto de Ciências Biológicas*
* **Luis Guimarães** - *Universidade Federal do Pará, Instituto de Ciências Biológicas*
* **Rommel Thiago Jucá Ramos** - *Universidade Federal do Pará, Instituto de Ciências Biológicas*

Use araujopa@gmail.com or rommelthiago@gmail.com for comments and questions.

## License
This project is licensed under the MIT License.

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