On the detection and abundance of large repeats in prokaryote genomes

Todd Treangen

De novo repeat detection tools help to bridge the widening gap
between newly sequenced genomes and the repeats found in annotation
databases. While there exist software tools for detecting pairwise
repeats, software tools for direct construction of repeat families
while allowing for substitutions and indels for accurate repeat
boundary prediction are lacking. We thus propose a novel software tool
called Repeatoire based on an efficient local multiple alignment
heuristic that will be discussed. Using Repeatoire, we have recently
conducted a survey of the abundance of repetitive DNA in nearly 700
prokaryote chromosomes by searching for all large repeats > 300 nt.
Results of this study will be presented.