ActDES-a Curated Actinobacterial Database for Evolutionary Studies

Scripts used in the curated database of 612 high quality actinobacterial genomes from 80 genera, chosen to represent a broad phylogenetic group with equivalent genome re-annotation.

Direct to JupyterNotebook

Download genome annotations from Zenodo

Annotation, nucleotides and aminoacid data for 612 genomes in ActDES have been deposited at ZENODO repository with the following doi:

Databases can be donwloaded with these links:

• Annotations
• Bindings
• Aminoacid Fasta
• Nucleotide Fasta

Annotation and Binding files are needed to obtain the frecuencies table. Aminoacids and nucleotide fasta files are provided just in case users may consider them useful.

Run ActDes to get abundance table

• Download Annotations and Bindings databases.
• Download perl script F1_FunctionCountBindings.pl
• With the script and databases at the same directory, please decompress both databases.
  untar
untar
• Calculated abundance tables
  perl F1_FunctionCountBindings.pl ID_all_species12042018
  

New data base from other RAST genomes

https://github.com/nselem/myrast

docker run -i -t -v $(pwd):/home nselem/myrast /bin/bash

1.NCBI_and_RAST.pl
F0_ExtractFiles.pl

• Decompress files
  perl F0_ExtractFiles.pl