Published June 29, 2023
| Version v2
Journal article
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Design and validation of a PCR screen for γ-butyrolactone-like regulatory systems in Streptomyces
Description
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.
- analysis_data_and_script.zip:
- cblaster output data
- search_ScbA_ScbR_600.txt - cblaster output file
- extracted_clusters_cblaster - gbk files of all clusters obtained using cblaster extract
- all_sequences.fasta - amino acid sequences of all proteins in the extracted clusters
- R markdown "Analysis script.rmd", which also contains some instructions for some bash operations using seqkit and grep
- intermediary files generated:
- ScbA_divergent_genes.txt - IDs of ScbA genes in divergent pair
- ScbR_divergent_genes.txt - IDs of ScbR genes in divergent pair
- ScbA_divergent.fasta - sequences of ScbA genes in divergent pair
- ScbR_divergent.fasta - sequences of ScbR genes in divergent pair
- ETxRx_containing_ScbA_list.txt - list of IDs of ScbA homologs containing ETxRx motif in divergent pair
- YFHx_containing_ScbR_list.txt - list of IDs of ScbR homologs containing YFHx motif in divergent pair
- ETxRx_containing_gbk_list.txt - list of extracted cluster genbank files containing ScbA homolog with ETxRx motif in divergent pair
- 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).
Files
analysis_data_and_script.zip
Files
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