#Bioinformatics course project
Finding riboswitches in Lactococcus lactis subsp. cremoris MG1363 Currently 24 Riboswitches are know, many riboswitch finding algorithms try to find new ones by homology search. although this is usefull across species it is unlikely to find completely new riboswitches. this project aims at finding new riboswitches not based on the conserverd functional aptamer, but by the expression platform, containg the regulatory terminator. to find this i though that a mimic of polymerase might be usefull, as it comes closer to what happens in reality. instead of what most people have used before by inputting the full RNA seq. this should show a terminator folding around the end -'3 end of the sequence. by using additional terminator search algorithm these are easier to find.
additonal programs and modules: mfold-3.6 --> http://unafold.rna.albany.edu/?q=mfold/download-mfold pygame --> http://www.pygame.org/hifi.html note* if using py3 make sure you have v1.9.2 pre
first few .py scripts are for reformatting the starting files i had. collectingGeneseq splitfasfile combineLocusfile
the rest is used to mimic polymerase run mfold, change file format (pdf to png) and then pygame.
TODO: optimally the additionally found terminator sequences would be highlighted in the .pdf mfold creates. after two days of trying i concluded that this would be really hard and required chaning the code of mfold. also tried additional ct to pdf drawing programs, stumbeld on the same problem. now the info is shown in the pygame screen. However, have not reformatted and searched trough the terminator.txt file.
note* you will need to change the directories in the .py scripts, as they are catered for my pc in another directory.