Experiments for ProtHint and GeneMark-EP/EP+ projects

Tomas Bruna, Alexandre Lomsadze, Mark Borodovsky

Georgia Institute of Technology, Atlanta, Georgia, USA

Reference: GeneMark-EP and -EP+: automatic eukaryotic gene prediction supported by spliced aligned proteins

Overview

This repository contains documentation of experiments, data and results for ProtHint and GeneMark-EP/EP+ projects.

Program Versions

All experiments in this folder were run with GeneMark-ES/EP/ET version 5.57_lic and ProtHint version v2.3.0. To reproduce the experiments, install these versions of the programs into bin/gmes and bin/ProtHint folders.

Versions of DIAMOND and Spaln within ProtHint were 0.9.24 and 2.3.3d, respectively.

• GeneMark suite is available at: http://topaz.gatech.edu/GeneMark/license_download.cgi
• ProtHint is available at: https://github.com/gatech-genemark/ProtHint/releases

Example of a full run

To run the entire GeneMark-EP+ pipeline with a single command, use:

cd full_run_example
../bin/gmes/gmes_petap.pl --seq ../Drosophila_melanogaster/data/genome.fasta.masked \
    --EP --dbep ../Drosophila_melanogaster/data/family_excluded.fa --verbose --cores=16

Follow the instructions in Drosophila_melanogaster/data folder to prepare genome and protein data.

If the matching version of GeneMark-EP+ was used, the result should match the result stored in full_run_example/expected_genemark.gtf. You can verify the match with:

./bin/compare_intervals_exact.pl --f1 full_run_example/expected_genemark.gtf --f2 \
    full_run_example/genemark.gtf --verbose

The percentage of unique CDS in either of the results should be < 0.05%. Minor fluctuations are possible, depending on the hardware.

The example uses D. melanogaster with proteins from species outside of the same taxonomical family.

In the rest of the experiments, GeneMark-ES, ProtHint, and GeneMark-EP+ are run separately to evaluate different aspects of the programs. However, all results in species/{}_excluded/EP/plus can be reproduced with the same single command which was used to generate the result in full_run_example folder.

Folder structure

The core folder structure for all tested species looks as follows:

.
├── bin                                   # Scripts for result generation and analysis
├── OrthoDB                               # Info about OrthoDB species/proteins
├── domains                               # Scripts and data for conserved domain analysis
├── full_run_example                      # Example of a full GeneMark-EP+ run
├── species_1                             # A test species
│   ├── annot                             # Annotation folder
│   │   ├── annot.gtf                     # Processed annotation
│   │   ├── pseudo.gff3                   # Coordinates of pseudogenic regions
│   ├── data                              # Folder with softmasked genome and input proteins
│   │   ├── genome.fasta.masked           # Softmasked genome
│   │   ├── {}_excluded.fa                # Input proteins with {} taxonomical level excluded
│   ├── bin                               # Scripts specific for this species
│   ├── ES                                # GeneMark-ES run
│   ├── ET                                # GeneMark-ET run
│   ├── varus                             # VARUS run
│   ├── {}_excluded                       # Results at a certain protein exclusion level {}
│   │   ├── prothint.gff                  # All reported ProtHint hints
│   │   ├── evidence.gff                  # High-Confidence ProtHint hints
│   │   ├── cmd.log                       # Command used to run this ProtHint run
│   │   ├── graphs                        # Visualizations relevant to this ProtHint run
│   │   ├── EP                            # Results of GeneMark-EP/EP+
│   │   │    ├── train                    # GeneMark-EP run
│   │   │    ├── plus                     # GeneMark-EP+ run
│   ├── extra_runs                        # Folder with additional ProtHint/EP runs (if any)
│   ├── accuracy_tables                   # Tables with experiment results
│   ├── EP+_results_visualization         # Figures visualizing EP+ results
│   ├── README.md                         # Readme with species specific information
├── species_2                             # Another test species
├── ...
├── species_n                             # Another test species
└

Specific ProtHint/GeneMark-EP folders may contain extra folders with additional experiments. In such cases, the experiments are documented within the species README file.