igorbonadio/myop

MYOP

MYOP - Make Your Own Predictor

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

Software Requirement

1. ToPS
2. SegSeq
3. Git
4. Perl - ForkManager
5. BioPerl
6. Linux or MacOSX

Installing MYOP

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

1. MYOP is available from our GitHub repository.

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

2. Copy the myop folder to /usr/local/ folder.

   sudo cp -r myop /usr/local
   

3. 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

1. Download the C. elegans model

   Pre-trained C. elegans model

2. Uncompress the tarball

   tar zxvf celegans.tar.gz
   

3. Download the fasta file

   FASTA file

4. 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

1. Download the GTF and the Fasta file

• GTF file
• Fasta file

2. 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>