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
   

Predicting genes

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

myop-predict.pl -p <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>

[1] The default model template is located at https://github.com/myopdev/myopTemplates.git

Pre-trained Models

MYOP provides the following pre-trained gene model, feel free to download it.

Download all models

• All pre-trained models

Plants

1. A. thaliana
2. O. sativa
3. Z. mays

Insect

1. D. melanogaster

Mammals

1. H. sapiens
2. M. musculus
3. R. norvegicus

Parasite

1. P. falciparum

Fish

1. D. rerio

Nematodes

1. C. elegans