id	author	title	date	pages	extension	mime	words	sentences	flesch	summary	cache	txt
cord-308331-55ge7kmr	Routh, Andrew	Discovery of functional genomic motifs in viruses with ViReMa–a Virus Recombination Mapper–for analysis of next-generation sequencing data	2013-10-09		.txt	text/plain	6014	285	52	Using ViReMa, we demonstrate that by mapping the distribution and frequency of recombination events in the genome of flock house virus (FHV), we can discover de novo functional genomic motifs required for viral replication and encapsidation. Here, segments at the 5 0 and the 3 0 end of a complex recombination event have been mapped to nt 500-550 and nt 1040-1080 of FHV RNA 1, but there remain a small number of trimmed nucleotides in the middle. We generated 5 043 791 synthetic reads containing 99 033 unique recombination events and aligned these reads to the FHV genome with ViReMa using a seed length of 20 nt. Our analysis of FHV demonstrates that by isolating a small number of virus particles, deep sequencing the encapsidated RNA and mapping the positions of recombination events, functional RNA motifs can be discovered.	./cache/cord-308331-55ge7kmr.txt	./txt/cord-308331-55ge7kmr.txt