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acquisition_cost_tet_analysis

Analysis scripts for tetracycline operon

readMe.txt author: Shahd ElNaggar

  1. plasmids_used.xlsx contains the plasmid metadata.
  2. CDS_extract.py BLASTp plasmid proteins against representative tetA and tetR sequences; saves tetA/R nucleotide sequences in multi-fasta; aligns sequences using ClustalW; generates list of tetA/R locus tags in genbank files.
  3. tet_operon.py uses locus tags generated by step (1) to extract nucleotide sequence of tetracycline operon from genbank files; it also creates a file containing tetA start positions.
  4. ori_BLAST.sh to BLAST plasmids against oriC/T databases.
  5. oriC_tet.py calculates distance between origin of transfer/replication and tetA gene to create a csv file with distances for each gene.

dependencies: BioPython, ClustalW, BLAST