MYOP - Make Your Own Predictor

MYOP is a customizable ab initio gene finding system that facilitates the customization of different strategies.

Software Requirement

Installing MYOP

After you have installed the required software, you can install MYOP by following the instructions below:

MYOP is available from our GitHub repository.

git clone https://github.com/myopdev/myop.git

Copy the myop folder to /usr/local/ folder.
```
sudo cp -r myop /usr/local
```

Add the following line at the end of the .profile file.

export PATH=$PATH:/usr/local/myop/scripts:/usr/local/myop/bin

Predicting genes

You can use the program myop-predict to predict protein-coding genes. This program receives the directory <model> of a trained gene model and a <fasta file>.

myop-predict -g <model> -f <fasta file> > out.gtf

Tutorial

Download the C. elegans model

Pre-trained C. elegans model
Uncompress the tarball
```
tar zxvf celegans.tar.gz
```
Download the fasta file

FASTA file

Execute the myop-predict.pl program

myop-predict.pl -p celegans  -f test.fa > out.gtf

Training gene models

You can use the program myop-train.pl to train a new gene model. This program receives a <fasta file> and an associated <GTF file>. This program will download a template that contains a pre-configured model from a Git repository[1]. It returns a directory that will contain the trained gene model.

myop-train.pl -g <gtf file> -f <fasta file> -o <output directory>

Tutorial

Download the GTF and the Fasta file

Execute the myop-train.pl

 myop-train.pl -g ce6.gtf -f ce6.fa -o celegans

Specifying a different model template

To specify a different model template, you can use the option -r

myop-train.pl -r <a customized model template> -g <gtf file> -f <fasta file> -o <output directory>