Transcriptome reconstruction bacteria

This project includes perl scripts to perform transcriptome reconstruction in bacteria (operons and UTRs). The software was applied to the transcriptome reconstruction of the species Methanococcoides burtonii, if you use it please refer to the following paper (Taha et al., Single TRAM domain RNA-binding proteins in Archaea: functional insights from Ctr3 from the Antarctic methanogen Methanococcoides burtonii - Submitted).
The approach used is based on previous results:
- Campanaro S, et al. The transcriptional landscape of the deep-sea bacterium Photobacterium profundum in both a toxR mutant and its parental strain. BMC Genomics. 2012; 13:567.
It uses as input the coverage files generated by the software ORA (https://sourceforge.net/projects/transcriptomeassemblyora/files/) (Sardu A, Treu L, Campanaro S. Transcriptome structure variability in Saccharomyces cerevisiae strains determined with a newly developed assembly software. BMC Genomics. 2014; 15:1045.)