id	author	title	date	pages	extension	mime	words	sentences	flesch	summary	cache	txt
cord-299944-1e44usl6	Gardner, Shea N.	Multiplex Degenerate Primer Design for Targeted Whole Genome Amplification of Many Viral Genomes	2014-08-03		.txt	text/plain	4147	175	52	The major difference is that it begins with a consensus sequence containing degenerate bases and selects primers with fewer than 3 or 4 degenerate bases, so that in the end a majority of strains are amplified, 2 Advances in Bioinformatics Table 1 : Summary of average lengths, number of sequences, and percentage of conserved bases in a multiple sequence alignment (with MUSCLE [5] ), and number of tiled primers required for the short and long amplicon settings. The method here differs in that it takes the full multiple sequence alignment as input rather than a consensus, and it seeks to automatically design a minimal, degenerate set of multiplex compatible primers to amplify all the strains for a given region in a single reaction. The run tiled primers process can be summarized as follows: split a multiple sequence alignment into overlapping regions, and for each region design a degenerate multiplex set of primers that in combination amplify that region in all strains with as few primers as possible.	./cache/cord-299944-1e44usl6.txt	./txt/cord-299944-1e44usl6.txt