AUTOMATION OF THE PROCESS OF PREDICTING THE SSR AS A PHASE VARIABLE WITHIN THE ENTIRE N. MENINGITIDIS GENOMEShaymaa Fouad Rasheed Al Khazraji and Mohammad Abdul Rahmman Al-Maeni
The abundance of repeat tracts along with genome of commensal and pathogenic N. meningitidis encourages us to think about a way of predicting the SSR that leads into phase variable mechanism. This prediction has to be automated using different language skills. Therefore our aim was to automate the process of predicting the SSR that leads into a phase variable mechanism relying on different criteria. These criteria were the length, polymorphic, instability and the value of Z score using a Markov model and synonymous shuffling model and the position of SSR within the gene or promoter. Perl script along with cgi and html was used for this purpose. Our automation program can detect three different categories for the SSR that leads into a phase variation mechanism which is weak, moderate and strong putative phase variable gene. We strongly recommended providing a good evidence for our model as it works correctly using experimental work.