A general computational model for predicting ribosomal frameshifts in genome sequences

Programmed ribosomal frameshifts are frequently used by RNA viruses to synthesize a single fusion protein from two or more overlapping open reading frames. We previously developed a program called FSFinder for predicting -1-1 and +1+1 frameshifts for Windows systems. With our new web application and web service called FSFinder2, users can predict frameshifts of any type from any web browser and operating system. We tested it on Shewanella oneidensis MR-1, for which exact frameshift sites are not known. FSFinder2 is the first program capable of finding frameshifts of general type and it is a powerful tool for predicting and analyzing genes that utilize frameshifts for their expression. FSFinder2 is available at http://wilab.inha.ac.kr/FSFinder.