Linux GUI app to codon optimize many single-fasta files with coding sequences , using many taxonomy ids

Related tags

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Overview

codon_optimize_cds_with_many_taxids_singlefasta DOI

Linux GUI app to codon optimize many single-fasta files with coding sequences, using many taxonomy ids

Depedences

  1. linux OS (tested on ubuntu 20.04 LTS)
  2. python 3.8.2 or later
  3. anaconda or miniconda
  4. Gooey conda install -c conda-forge gooey(if you get errors during installation or runtime try installing gtk sudo apt-get install libgtk-3-dev)
  5. biopython pip install biopython
  6. pandas pip install pandas
  7. dnachisel pip install dnachisel

linux desktop app installation

  1. open a linux text editor and edit in the python file the shebang line (to find where python is type in the terminal which python3)
  2. convert to executable with chmod +x codon_optimize_cds_with_many_taxidS_singlefasta_gui.py
  3. open a linux text editor and edit the PATHs in the .desktop file
  4. move the file to /usr/share/applications
  5. reboot your machine

Output

The output single-fasta files will have the same prefix as the input ones and as suffix the taxonomy ids of the organisms they are codon optimized for

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