DOI: 10.6084/m9.figshare.21641612.v1
title: Datasets for Lupo et al. (2022) Origin and Evolution of Pseudomurein Biosynthetic Gene Clusters

description: <pre><code>Lupo et al. 2022 Pseudomurein: Archive content for v1</code></pre>
<strong>Overview</strong>
<pre><code>... 61 directories, 769 files</code></pre>

 README.md: this file.
 <code>command-line.sh</code>: examples of bash commands to use or generate the files stored in this archive.

10-archaeal-proteomes
This directory contains an archive (<code>.tar.gz</code>) consisting of FASTA (<code>.faa</code>) files of the 10 organisms used by OrthoFinder.
alphafold
List of ZIP (<code>.zip</code>) files containing the raw results of AlphaFold predictions and Consurf results.
archaeal-genomes
This directory contains an archive (<code>.tar.gz</code>) consisting of 819 FASTA (<code>.faa</code>) files corresponding to the archaeal database.
bacterial-genomes
This directory contains an archive (<code>.tar.gz</code>) consisting of 598 FASTA (<code>.faa</code>) files corresponding to the bacterial database.
config
This directory contains two configuration files (<code>.yaml</code>) used by the <code>classify-ali.pl</code> perl script from Bio::MUST modules:

 <code>classifier.yaml</code> is the configuration file used to filter the 6,321 orthologous groups (OGs).
 <code>five_org_classifier.yaml</code> is the configuration file used to filter the OGs after the round of Forty-Two TBLASTN.

BLASTP
List of configuration files to run Forty-Two BLASTP (FILTERING OF CANDIDATE PROTEINS; see figure S1 in the main manuscript).
TBLASTN
List of configuration files to run Forty-Two TBLASTN (FILTERING OF CANDIDATE PROTEINS; see figure S1 in the main manuscript).
NCBI_CCD
List of HMM (<code>.hmm</code>) profile files downloaded from NCBI CDD database and corresponding HMM search (<code>.hmms</code>) files.
ompapa-results
Raw Ompa-Pa results associated with NCBI CDD HMM profiles.
ompapa
This directory contains a list of the OGs that have passed the taxonomic filter (see <code>config</code> sections).
alignments
List of alignments in FASTA format of the OGs included in the <code>retained_OGs.lis</code> file (see <code>ompapa</code> section).
bacterial_db
Results of ompapa analyses against the bacterial database. This directory contains two sub-directories:

 <code>hmms</code> that contains a list of HMM search (<code>.hmms</code>) files.
 <code>ompapa-results</code> that contains raw ompapa results.

hmm_profiles
List of HMM (<code>.hmm</code>) profiles of the OGs included in the <code>retained_OGs.lis</code> file (see <code>ompapa</code> section).
prokaryotic_db
Results of ompapa analyses against the prokaryotic database. This directory contains two sub-directories:

 <code>hmms</code> that contains a list of HMM search (<code>.hmms</code>) files.
 <code>ompapa-results</code> that contains raw ompapa results.

orthologous-groups
This directory contains an archive (<code>.tar.gz</code>) consisting of 6,321 FASTA (<code>.fasta</code>) files corresponding to the OGs generated by OrthoFinder.
predictions
This directory contains three sub-directories:

 <code>interproscan</code> that contains raw InterProScan results.
 <code>signalp5</code> that contains raw SignalP5 results.
 <code>tmhmm</code> that contains raw TMHMM results.

For the consolidated results, see Table S1 in the main manuscript.
prokaryotic-genomes
This directory contains a list of assembly accessions of the 80,490 organisms from the prokaryotic database.
regulon
This directory contains all the data needed to reproduce the â€˜regulon pipelineâ€™ (see supplementary data from the main manuscript). All the command lines are included in the <code>command_line_regulon.sh</code> file.
scripts
This directory contains various perl scripts used to generate some of the files stored in this archive (see <code>command-line.sh</code> file).
taxdump
Mirror of the NCBI Taxonomy used in this study (downloaded on 4th of May 2020).
trees
This directory contains three sub-directories:

 <code>atp-grasp</code>
 <code>mray-family</code>
 <code>mur-family</code>

All the sub-directories contains tree (<code>.tre</code>) files presented in the main manuscript and corresponding raw IQ-TREE (<code>.ckp.gz</code>) results. They also contain various files needed to reproduce the phylogenetic analyses (see <code>command-line.sh</code> file).
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