BioGenie

BioGenie is a complete bioinformatics command line tool for macOS, GNU Linux and MS Windows, written in C++.

Important

The Windows version is not being maintained at the moment. Last available version: 0.14.0(https://github.com/mikeph52/BioGenie/releases/tag/v.0.14.0). Use WSL(Windows Subsystem for Linux) instead.

It currently supports fasta formats(.fasta, .fa).

• To run the app, simply type:

biogenie <function> <filename>

• For example, to calculate GC percentage:

biogenie -gc example.fasta

Documentation

BioGenie uses functions to execute different tools for different applications. Read Documentation for more information (References included).

• Get the complement DNA sequence ---> "-c".
• Get the reverse complement DNA sequence ---> "-rc".
• Get the codon number ---> "-nc".
• Get the mRNA ---> "-t".
• GC percentage calculation ---> "-gc".
• Generate the aminoacids(Protein chain) ---> "-p".
• Separate different sequencies in a FASTA file ---> "-ss".
• Print the different sequence headers from a FASTA file ---> "-sh".
• Trim DNA sequence ---> "-tr".
• Calculate the Number of Base Pairs(bp) ---> "-bp".
• Get the purine/pyrimidine ratio --> "-pp".
• Calculate melting temperature (Tm) of DNA sequences using the Wallace Rule(only valid for oligos <20bp) ---> "-mt1".
• Calculate melting temperature (Tm) of DNA sequences using the SantaLucia 1998 nearest-neighbor method ---> "-mt2".
• Coloured cDNA sequence ---> "-cc".
• Coloured DNA sequence ---> "-sc".
• Get the Open Reading Frame(ORF) ---> "-orf".
• Generate cDNA sequence FASTA ---> "-cw".
• Generate Reverse cDNA sequence FASTA ---> "-rcw".
• Generate mRNA sequence FASTA ---> "-tw".
• Calculate Codon Usage Bias(CUB) ---> "-cub".
• Export Codon Usage Bias(CUB) to CSV file ---> "-wcub".
• Custom preset pipeline 1 ---> "-pip1".
• Custom preset pipeline 2 ---> "-pip2".

More functions will be added in the future.

Installation

GNU Linux

• Download BioGenie from Releases, or with wget:

wget https://github.com/mikeph52/BioGenie/releases/download/v.0.23.0/biogenie_linux_0.23.0

• Run "chmod +x" first(Replace 0.x.x with the correct version).

sudo chmod +x biogenie_linux_0.x.x

• Move it to bin folder by executing the following command:

sudo mv biogenie_linux_0.x.x /usr/local/bin/biogenie

macOS

• Download BioGenie from Releases, or with curl:

curl -l https://github.com/mikeph52/BioGenie/releases/download/v.0.23.0/biogenie_macos_0.23.0

• Run "chmod +x" first(Replace 0.x.x with the correct version).

sudo chmod +x biogenie_macos_0.x.x

• Move it to bin folder by executing the following command:

sudo mv biogenie_macos_0.x.x /usr/local/bin/biogenie

MS Windows

It requires Windows 10 or later.

• Download BioGenie from Releases.
• Add the executable to PATH(https://stackoverflow.com/questions/44272416/add-a-folder-to-the-path-environment-variable-in-windows-10-with-screenshots)
• Run from powershell. There's also a GUI Version Available on Alpha testing.

Caution

This is an Alpha testing version. It is not functional. Not for scientific use.

Important

The Windows version is not being maintained at the moment. Last available version: 0.14.0(https://github.com/mikeph52/BioGenie/releases/tag/v.0.14.0). Use WSL(Windows Subsystem for Linux) instead.

Changelog:

• 0.23.0: DNA sequence with color added.
• 0.22.0: Base Pair calculation added to Pipeline 2. Minor bugs fixed.
• 0.21.0: Base Pair calculation added. Minor bugs fixed.
• 0.20.0: Codon Usage Bias(CUB) calculation and export to csv function added.
• 0.19.0: (#15) Minor bugs fixed.
• 0.18.0: Generate mRNA FASTA added. Minor format bugs fixed.
• 0.17.3: (#13) Issue Fixed.
• 0.17.2: (#12) Issue Fixed.
• 0.17.0: Generate cDNA FASTA and reverse compliment FASTA function added.
• 0.16.0: Open Reading Frames finder function added. Minor bugs fixed.
• 0.15.0: (#9) Fixed Melting Temperature Calculator functiion. SantaLucia 1998 nearest-neighbor method added as "-mt2". Pipeline 2 function also fixed. Now uses SantaLucia 1998 nearest-neighbor method for more accurate calculations. Minor bugs fixed.
• 0.14.0: Coloured cDNA sequence. Minor adjustments made and bugs fixed.
• 0.13.0: Purine/pyrimidine ratio and Melting temperature(Tm) calculator functions added. Preset Pipeline 2 added. Minor format fixes.
• 0.12.2: Minor format fixes.
• 0.12.0: (#7) Protein function output fixed, "Pipeline 1" added and minor bugs fixed.
• 0.11.0: FASTA file verification and integrity checker added.
• 0.10.0: (#6) FASTA sequence header print function added. DNA trimmer function added. Windows support added. Minor bugs fixed and quality of life improvements.
• 0.9.0: Linux support added. FASTA sequencies separator added and minor bugs fixed.
• 0.8.0: Protein chain option added and minor bugs fixed.
• 0.7.0: (#4) Documentation fixed.
• 0.6.0: (#3) Documentation added
• 0.5.0: (#2) Function operator added.
• 0.4.0: (#1) Reverse complement DNA function added.
• 0.3.0: Number of codone calculator added.
• 0.2.3: GC calculator, complimentary DNA and transcripted RNA functions added.
• 0.1.0: First Version.