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C++.\n\n\u003cimg width=\"1002\" height=\"770\" alt=\"Image\" src=\"https://github.com/user-attachments/assets/4dfb77db-721d-42e0-ade9-73115f12057e\" /\u003e\n\n\nIt currently supports fasta formats(.fasta, .fa).\n- To run the app, simply type:\n```\nbiogenie \u003cfunction\u003e \u003cfilename\u003e\n```\n- For example, to calculate GC percentage:\n```\nbiogenie -gc example.fasta\n```\n\n## Documentation\nBioGenie uses functions to execute different tools for different applications.\nRead [Documentation](documentation.md) for more information (*References included*).\n- Get the complement DNA sequence ---\u003e \"-c\".\n- Get the reverse complement DNA sequence ---\u003e \"-rc\".\n- Get the codon number ---\u003e \"-nc\".\n- Get the mRNA ---\u003e \"-t\".\n- Motif search ---\u003e \"-mf\".\n- Ambiguous bases statistics ---\u003e \"-amb\".\n- GC percentage calculation ---\u003e \"-gc\".\n- Generate the aminoacids(Protein chain) ---\u003e \"-p\".\n- Generate the Protein chain with color ---\u003e \"-pc\".\n- Separate different sequencies in a FASTA file ---\u003e \"-ss\".\n- Print the different sequence headers from a FASTA file ---\u003e \"-sh\".\n- Trim DNA sequence ---\u003e \"-tr\".\n- Calculate the Number of Base Pairs(bp) ---\u003e \"-bp\".\n- Get the purine/pyrimidine ratio --\u003e \"-pp\".\n- Calculate melting temperature (Tm) of DNA sequences using the Wallace Rule(only valid for oligos \u003c20bp) ---\u003e \"-mt1\".\n- Calculate melting temperature (Tm) of DNA sequences using the SantaLucia 1998 nearest-neighbor method ---\u003e \"-mt2\".\n- Calculate the Isoelectric Point of a protein ---\u003e \"-pi\".\n- Calculate the molecular weight of a protein(kDa) ---\u003e \"-mw\".\n- Calculate the Extinction Coefficient of a protein ---\u003e \"-ec\".\n- Coloured cDNA sequence ---\u003e \"-cc\".\n- Coloured DNA sequence ---\u003e \"-sc\".\n- Get the Open Reading Frame(ORF) ---\u003e \"-orf\".\n- Generate cDNA sequence FASTA ---\u003e \"-cw\".\n- Generate Reverse cDNA sequence FASTA ---\u003e \"-rcw\".\n- Generate mRNA sequence FASTA ---\u003e \"-tw\".\n- Calculate Codon Usage Bias(CUB) ---\u003e \"-cub\".\n- Export Codon Usage Bias(CUB) to CSV file ---\u003e \"-wcub\".\n- Calculate Hydrogen Bonds of dsDNA ---\u003e \"-hb\".\n- Custom preset pipeline 1 ---\u003e \"-pip1\".\n- Custom preset pipeline 2 ---\u003e \"-pip2\".\n- Custom preset pipeline 3 ---\u003e \"-pip3\".\n\n\nMore functions will be added in the future.\n\n\u003e [!NOTE]\n\u003e _If you have any suggestions for new features or a bug encountered, create an Issue or send me a message at: mikeph526@outlook.com. I'm happy to help._\n\n## Installation\n### GNU Linux\n- Download BioGenie from Releases, or with wget:\n```\nwget https://github.com/mikeph52/BioGenie/releases/download/v.0.27.0/biogenie_linux_0.27.0\n``` \n- Run \"chmod +x\" first(Replace 0.x.x with the correct version).\n```\nsudo chmod +x biogenie_linux_0.x.x\n``` \n- Move it to bin folder by executing the following command:\n```\nsudo mv biogenie_linux_0.x.x /usr/local/bin/biogenie\n```\n- If you need to build from source:\n```\ngit clone https://github.com/mikeph52/BioGenie.git\ng++ main.cpp -o biogenie\nsudo mv biogenie /usr/local/bin/\n```\n### macOS\n- Download BioGenie from Releases, or with curl:\n```\ncurl -l https://github.com/mikeph52/BioGenie/releases/download/v.0.27.0/biogenie_macos_0.27.0\n``` \n- Run \"chmod +x\" first(Replace 0.x.x with the correct version).\n```\nsudo chmod +x biogenie_macos_0.x.x\n``` \n- Move it to bin folder by executing the following command:\n```\nsudo mv biogenie_macos_0.x.x /usr/local/bin/biogenie\n```\n- If you need to build from source(probably not):\n```\ngit clone https://github.com/mikeph52/BioGenie.git\ng++ -std=c++17 main.cpp -o biogenie\nsudo mv biogenie /usr/local/bin/\n```\n### MS Windows (Deprecated)\n\u003e [!IMPORTANT]\n\u003e _The Windows version is not being maintained and probably never will. Last available version: 0.14.0(https://github.com/mikeph52/BioGenie/releases/tag/v.0.14.0). Use WSL(Windows Subsystem for Linux) instead._\nIt requires Windows 10 or later.\n- Download BioGenie from Releases.\n- Add the executable to PATH(https://stackoverflow.com/questions/44272416/add-a-folder-to-the-path-environment-variable-in-windows-10-with-screenshots)\n- Run from powershell.\nThere's also a GUI Version Available on Alpha testing.\n\u003e [!CAUTION]\n\u003e This is an Alpha testing version. It is not functional. Not for scientific use. I don't think it is possible to make and maintain a gui version for windows. The code is complicated already. It's time to move on.\n\n## Changelog:\n- 0.27.0:\nMulti core support added for pip1, pip2 and pip3(https://github.com/mikeph52/BioGenie/issues/30), (https://github.com/mikeph52/BioGenie/issues/31). Ambiguous bases statistics added. Execution timer added. Minor bugs fixed.\n\n- 0.26.0:\nHydrogen bonds calculator and protein chain with color added.\n- 0.25.0:\nProtein mollecular weight, isoelectric point, extinction coeficient and pipeline 3 added. Issues https://github.com/mikeph52/BioGenie/issues/25, https://github.com/mikeph52/BioGenie/issues/27 fixed. Major performance improvements made. Minor bugs fixed. \n- 0.24.0:\nMotif search added. Issues https://github.com/mikeph52/BioGenie/issues/19, https://github.com/mikeph52/BioGenie/issues/21, https://github.com/mikeph52/BioGenie/issues/23, https://github.com/mikeph52/BioGenie/issues/24 fixed. Minor formatting issues fixed.\n- 0.23.0:\nDNA sequence with color added.\n- 0.22.0:\nBase Pair calculation added to Pipeline 2. Minor bugs fixed.\n- 0.21.0:\nBase Pair calculation added. Minor bugs fixed.\n- 0.20.0:\nCodon Usage Bias(CUB) calculation and export to csv function added.\n- 0.19.0:\n(https://github.com/mikeph52/BioGenie/issues/15)\nMinor bugs fixed.\n- 0.18.0:\nGenerate mRNA FASTA added. Minor format bugs fixed.\n- 0.17.3:\n(https://github.com/mikeph52/BioGenie/issues/13)\nIssue Fixed.\n- 0.17.2:\n(https://github.com/mikeph52/BioGenie/issues/12)\nIssue Fixed.\n- 0.17.0:\nGenerate cDNA FASTA and reverse compliment FASTA function added.\n- 0.16.0:\nOpen Reading Frames finder function added. Minor bugs fixed.\n- 0.15.0:\n(https://github.com/mikeph52/BioGenie/issues/9)\nFixed 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.\n- 0.14.0:\nColoured cDNA sequence. Minor adjustments made and bugs fixed.\n- 0.13.0:\nPurine/pyrimidine ratio and Melting temperature(Tm) calculator functions added. Preset Pipeline 2 added. Minor format fixes.\n- 0.12.2:\nMinor format fixes.\n- 0.12.0:\n(https://github.com/mikeph52/BioGenie/issues/7)\nProtein function output fixed, \"Pipeline 1\" added and minor bugs fixed.\n- 0.11.0:\nFASTA file verification and integrity checker added.\n- 0.10.0:\n(https://github.com/mikeph52/BioGenie/issues/6)\nFASTA sequence header print function added. DNA trimmer function added. Windows support added. Minor bugs fixed and quality of life improvements.\n- 0.9.0:\nLinux support added. FASTA sequencies separator added and minor bugs fixed.\n- 0.8.0:\nProtein chain option added and minor bugs fixed.\n- 0.7.0:\n(https://github.com/mikeph52/BioGenie/issues/4)\nDocumentation fixed.\n- 0.6.0:\n(https://github.com/mikeph52/BioGenie/issues/3)\nDocumentation added\n- 0.5.0:\n(https://github.com/mikeph52/BioGenie/issues/2)\nFunction operator added.\n- 0.4.0:\n(https://github.com/mikeph52/BioGenie/issues/1)   Reverse complement DNA function added.\n- 0.3.0:\nNumber of codone calculator added.\n- 0.2.3:\nGC calculator, complimentary DNA and transcripted RNA functions added.\n- 0.1.0:\nFirst Version.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmikeph52%2Fbiogenie","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmikeph52%2Fbiogenie","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmikeph52%2Fbiogenie/lists"}