Functional Association of Prokaryotic Virus Orthologous Groups: A Proof of Concept - Data
Dutilh, E. Bas
Raw data required to reproduce all intermediate results and thereby the final predictions.
These are used in the accompanying snakemake pipeline https://git.science.uu.nl/papanikos/pvogs_function.
This archive is automatically downloaded and files are extracted when executing the pipeline.
You can also download and extract the files manually.
Included files are:
- data/genomes/phages_refseq.fasta : A multifasta file with all phage genomes available on RefSeq , on 14/01/2020
- data/interactions/interactions.txt: A PSI-MI TAB file containing all interactions from IntAct, retrieved on 28/05/2019
- data/pvogs/all.hmm : All hmmer profiles for pVOGs, retrieved from http://dmk-brain.ecn.uiowa.edu/pVOGs/downloads on 13/01/2020
- data/pvogs/VOGProteinTable.txt: pVOGs occurrence on genomes used in the pVOGs paper, along with their annotation, retrieved on 16/01/2020
- data/taxonomy_db/taxa.sqlite.db: Taxonomy db created with ete3 toolkit with data retrieved on 16/05/2019
- data/taxonomy_db/taxa.traverse.pkl: Created automatically with ete3.
- data/md5sums.txt: md5sums for all files