Design and validation of a PCR screen for γ-butyrolactone-like regulatory systems in Streptomyces

This archive contains data related to the article "Design and validation of a PCR screen for γ-butyrolactone-like regulatory systems in Streptomyces" in Access Microbiology. 

• downloaded_genomes.txt: The list of the 2040 Streptomyces genomes downloaded by ncbi-genome-download and used in this analysis
• analysis_data_and_script.zip:

1. cblaster output data
   1. search_ScbA_ScbR_600.txt - cblaster output file
   2. extracted_clusters_cblaster - gbk files of all clusters obtained using cblaster extract
   3. all_sequences.fasta - amino acid sequences of all proteins in the extracted clusters
2. R markdown "Analysis script.rmd", which also contains some instructions for some bash operations using seqkit and grep
3. intermediary files generated:
   1. ScbA_divergent_genes.txt - IDs of ScbA genes in divergent pair
   2. ScbR_divergent_genes.txt - IDs of ScbR genes in divergent pair
   3. ScbA_divergent.fasta - sequences of ScbA genes in divergent pair
   4. ScbR_divergent.fasta - sequences of ScbR genes in divergent pair
   5. ETxRx_containing_ScbA_list.txt - list of IDs of  ScbA homologs containing ETxRx motif in divergent pair
   6. YFHx_containing_ScbR_list.txt - list of IDs of ScbR homologs containing YFHx motif in divergent pair
   7. ETxRx_containing_gbk_list.txt - list of extracted cluster genbank files containing ScbA homolog with ETxRx motif in divergent pair
   8. ETxRx_and_YFHx_containing_gbk_list.txt - list of extracted cluster genbank files containing ScbA homolog with ETxRx motif and ScbR homolog with YFHx motif in divergent pair, i.e. co-occurrence of motifs

• Sanger sequences (ending in .seq) of the PCR reactions
• The genomes of three newly sequenced Antarctic Streptomyces (illumina and nanopore hybrid assembly using unicycler).