DOI: 10.6084/m9.figshare.18544955
title: Datasets for Lupo et al. (2022) An extended reservoir of class-D beta-lactamases in non-clinical bacterial strains

description: <pre>Lupo et al. 2022: Archive content for v2Overview<pre><code>... 17 directories, 182 files </code></pre></pre><code>README.md</code>: this file.<code>command-line.sh</code>: examples of bash commands to use or generate the files stored in this archive.biosampleThis directory contains input and output files used to assign a “clinical” score to a BioSample report (…)bldb_oxaFile in <code>.fasta</code> format of the reference OXA-family sequences from the Beta-lactamase Database (BLDB) used for annotation with the <code>annotate.pl</code> perl script from Bio::MUST modules.genetic_environmentThis directory contains the list of bacterial assembly download links in <code>.csv</code> format to provide to GeneSpy and the list of contig accession numbers to download with the command-line <code>efetch</code> tool from the NCBI E-utilities.local_refseq_dbThe list of the assembly accession numbers of the local RefSeq database built on 7th of December 2017.ncbi_pathogenThis directory contains consolidated FASTA (<code>.fasta</code>) and TSV (<code>.tab</code>) files downloaded from the NCBI Pathogen Detection server (ftp://ftp.ncbi.nlm.nih.gov/pathogen/):<code>all-prot-nr.fasta</code><code>all_bla.tab</code>It also contains files associated to class-D beta-lactamases (…)oxa_familyThis directory contains the FASTA file <code>bla_d.fasta</code> with the 24,916 OXA-family protein selected with the <code>ompa-pa.pl</code> script and its deduplicated file <code>clst95_bla_d.fasta</code> and also the coordinates file <code>class_d98.bb</code> and the sequence accession identifier file <code>class_d98.idl</code> from <code>ompa-pa.pl</code>.alignmentsThree alignments of OXA-family proteins are available (…)treeThe <code>mapper.idm</code> is a TSV file that contains the short and corresponding long sequence identifiers used to rename sequences for booster and RAxML tree.boosterThis directory contains raw output files obtained from the booster web server in NEWICK format. <code>boosterweb_tbe_norm.nh</code>is the final tree file.consenseConsensus tree computed with <code>consense</code> (PHYLIP package) using the 100 replicate trees of RAxML<code>RAxML_bootstrap.classd-final-edit_188-RAXML-PROTGAMMALGF-100xRAPIDBP</code>.raxmlThis directory contains raw output files of RAxML in NEWICK format, computed from the reduced alignment <code>classd-final-edit_188.fasta</code>.oxa_family_clustersThis directory contains alignment files in FASTA format and the corresponding <code>.hmm</code> profile files for non-singleton clusters (representative sequences) (…)oxa_family_domainsThe 3510 unique OXA-family sequences and their corresponding taxonomy are available in FASTA format <code>3510_bla.fasta</code>and TSV format <code>3510_bla.tax</code> (…)phylogenetic_clusteringThis directory contains a templatized R script <code>mcl.script.R.tt</code> used to compute phylogenetic clustering, the ladderized rooted OXA-family tree used by the R script and its associated traits file.scriptsThis directory contains various perl scripts (…)sql_dbThis directory contains the <code>SQL</code> files for the results database (…)taxdump-20180208Mirror of the NCBI Taxonomy used in this study (downloaded on 8th of February 2018).<br>