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 thi...
Main Author: | |
---|---|
Format: | Article in Journal/Newspaper |
Language: | unknown |
Published: |
2023
|
Subjects: | |
Online Access: | https://zenodo.org/record/8272490 https://doi.org/10.5281/zenodo.8272490 |
id |
ftzenodo:oai:zenodo.org:8272490 |
---|---|
record_format |
openpolar |
spelling |
ftzenodo:oai:zenodo.org:8272490 2023-09-05T13:13:11+02:00 Design and validation of a PCR screen for γ-butyrolactone-like regulatory systems in Streptomyces Valentin Waschulin 2023-06-29 https://zenodo.org/record/8272490 https://doi.org/10.5281/zenodo.8272490 unknown doi:10.5281/zenodo.8094742 https://zenodo.org/record/8272490 https://doi.org/10.5281/zenodo.8272490 oai:zenodo.org:8272490 info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/legalcode info:eu-repo/semantics/article publication-article 2023 ftzenodo https://doi.org/10.5281/zenodo.827249010.5281/zenodo.8094742 2023-08-22T23:06:12Z 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: 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). Article in Journal/Newspaper Antarc* Antarctic Zenodo Antarctic |
institution |
Open Polar |
collection |
Zenodo |
op_collection_id |
ftzenodo |
language |
unknown |
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. 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: 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). |
format |
Article in Journal/Newspaper |
author |
Valentin Waschulin |
spellingShingle |
Valentin Waschulin Design and validation of a PCR screen for γ-butyrolactone-like regulatory systems in Streptomyces |
author_facet |
Valentin Waschulin |
author_sort |
Valentin Waschulin |
title |
Design and validation of a PCR screen for γ-butyrolactone-like regulatory systems in Streptomyces |
title_short |
Design and validation of a PCR screen for γ-butyrolactone-like regulatory systems in Streptomyces |
title_full |
Design and validation of a PCR screen for γ-butyrolactone-like regulatory systems in Streptomyces |
title_fullStr |
Design and validation of a PCR screen for γ-butyrolactone-like regulatory systems in Streptomyces |
title_full_unstemmed |
Design and validation of a PCR screen for γ-butyrolactone-like regulatory systems in Streptomyces |
title_sort |
design and validation of a pcr screen for γ-butyrolactone-like regulatory systems in streptomyces |
publishDate |
2023 |
url |
https://zenodo.org/record/8272490 https://doi.org/10.5281/zenodo.8272490 |
geographic |
Antarctic |
geographic_facet |
Antarctic |
genre |
Antarc* Antarctic |
genre_facet |
Antarc* Antarctic |
op_relation |
doi:10.5281/zenodo.8094742 https://zenodo.org/record/8272490 https://doi.org/10.5281/zenodo.8272490 oai:zenodo.org:8272490 |
op_rights |
info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/legalcode |
op_doi |
https://doi.org/10.5281/zenodo.827249010.5281/zenodo.8094742 |
_version_ |
1776203919693709312 |