Resources

Regulatory network

We have derived a new regulatory network based on experimental data and statistical approaches (Chiner-Oms et al. 2018).

You can download the network by clicking in the following link: regulatory_network

MTBC ancestor

The Mycobacterium tuberculosis complex most likely common ancestor derived as described in Comas et al. 2010.

You can download the fasta file by clicking in the following link:MTBC_ancestor.fas

Scripts

Insert deletions in a fasta file

It creates alternative fasta files with 7 different deletion ranges a target gene.
It takes as an input a fasta file containing a genome, an annotation file and a target gene. It generates 5 different fasta files for each deletion range (1 bp, 2-10 bp, 10-20 bp, 20-40 bp, 40-50 bp, 50-60 bp and 60-100 bp). The new fasta files are placed in the same folder containing the reference genome. Also a .txt file with a summary of the new files created is generated in the script folder. The following perl modules are necessary to run the code:

  • File::Path::Expand
  • BioPerl
  • Clone

Example:

perl fasta_insert_deletions.pl H37Rv.fas H37Rv.gff -g Rv0757

Download the perl code by clicking in the following link: fasta_insert_deletions.pl

In conjunction with the ART tool allows you to create simulated fastq files with random deletions in specific regions that could be used to test NGS analysis pipelines (publication pending).

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