Data mining for Recombinase-in-Trio (RIT) Elements

Advisor:
Nicole Ricker (Pathobiology)

RIT elements are a recently described class of mobile elements that are found in a broad diversity of bacterial genomes. Although initial studies have illustrated their potential for mobility, the mechanism for their movement has yet to be confirmed. For this one-semester project, the student will search the NCBI database for clusters of tyrosine recombinase genes corresponding with the three identified families that comprise a RIT element. The student will use this information to update the distribution of RIT elements in currently sequenced genomes, and to identify genomes containing multiple copies suggesting recent activity. The student will then write a program to identify the inverted repeats that flank the RIT elements, and to search for a palindromic sequence believed to be involved in their mobility.