MPI Simple Gene Finder Framework

Summary

In bioinformatics, gene finding refers to identifying regions of genomic DNA that encode genes. Gene finding includes protein-coding genes and RNA genes. Gene discovery is the first and one of the most critical steps in understanding the sequencing of a species' genome. However, the process of gene finding takes a lot of time. This program is a framework that can help us do gene finding job on multiple nodes using MPI.

Compile

Pre-request:

GCC/Clang++ (Support C++17/OpenMP)
OpenMPI Development pack
CMake
Make

For Ubuntu:

sudo apt install cmake make g++ openmpi-bin libopenmpi-dev

Compile Command

cmake .
make

Built Binary

There is a X64 Linux Build (openMPI) in folder: ./build/

Run

Single Node Version:

Usage: ./gene_finder --input INPUT_FILE_PATH --output OUTPUT_FILE_PATH [--pattern LABEL_PATTERN --output-line-width WIDTH --time]
    Default:
        LABEL_PATTERN = '%s | gene | frame=%d | LOC=[%d,%d]'
        WIDTH = 70

Mutiple Node (MPI) Versoin:

Usage: mpirun [MPI_ARGS] ./gene_finder_mpi --input INPUT_FILE_PATH --output OUTPUT_FILE_PATH [--pattern LABEL_PATTERN --output-line-width WIDTH]
    Default:
        LABEL_PATTERN = '%s | gene | LOC=[%d,%d]'
        WIDTH = 70

Here are sample run command sbatch script:

Development

Self Defined ORF Evaluation Function

All code for developing library are in ./gene_judge/ directory.

You can edit ./gene_judge/gene_judge.cpp to program you own gene identifing function.

Here are two other sample:

gene_judge_filter_all.cpp: Filter out all orfs.
gene_judge_get_all.cpp: Get all orfs.

Compile Self Defined ORF Evaluation Function

Go root directory of this repo, then:

cmake .
make gene_judge

It will genreate a dynamic linked library file. You can replace the file in build directory (.so or .dll) to the one you build.

Paper & Presntation

Distributed Framework for Gene Finding using Open-MPI

Presentation Slides

kaseidis/MPI_Simple_Gene_Finder