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
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
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:
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).