Dataset Open Access

Functional Association of Prokaryotic Virus Orthologous Groups: A Proof of Concept - Data

Pappas, Nikolaos; Dutilh, E. Bas


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    <subfield code="a">&lt;p&gt;Raw data required to reproduce all intermediate results and thereby the final predictions.&lt;/p&gt;

&lt;p&gt;These are used in the accompanying snakemake pipeline https://git.science.uu.nl/papanikos/pvogs_function.&lt;/p&gt;

&lt;p&gt;This archive is automatically downloaded and files are extracted when executing the pipeline.&lt;/p&gt;

&lt;p&gt;You can also download and extract the files manually.&lt;/p&gt;

&lt;p&gt;Included files are:&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;data/genomes/phages_refseq.fasta : A multifasta file with all phage genomes available on RefSeq , on 14/01/2020&lt;/li&gt;
	&lt;li&gt;data/interactions/interactions.txt: A PSI-MI TAB file containing all interactions from IntAct, retrieved on 28/05/2019&lt;/li&gt;
	&lt;li&gt;data/pvogs/all.hmm : All hmmer profiles for pVOGs, retrieved from http://dmk-brain.ecn.uiowa.edu/pVOGs/downloads on 13/01/2020&lt;/li&gt;
	&lt;li&gt;data/pvogs/VOGProteinTable.txt: pVOGs occurrence on genomes used in the pVOGs paper, along with their annotation, retrieved on 16/01/2020&lt;/li&gt;
	&lt;li&gt;data/taxonomy_db/taxa.sqlite.db: Taxonomy db created with ete3 toolkit with data retrieved on 16/05/2019&lt;/li&gt;
	&lt;li&gt;data/taxonomy_db/taxa.traverse.pkl: Created automatically with ete3.&lt;/li&gt;
	&lt;li&gt;data/md5sums.txt: md5sums for all files&lt;/li&gt;
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