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Advances in Bioinformatics
Volume 2014 (2014), Article ID 101894, 8 pages
Research Article

Multiplex Degenerate Primer Design for Targeted Whole Genome Amplification of Many Viral Genomes

1Computations, Lawrence Livermore National Laboratory (LLNL), Livermore, CA 94550, USA
2Physical and Life Sciences/Global Security, Lawrence Livermore National Laboratory (LLNL), Livermore, CA 94550, USA

Received 30 May 2014; Accepted 14 July 2014; Published 3 August 2014

Academic Editor: Paul Harrison

Copyright © 2014 Shea N. Gardner et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Supplementary Material

The data for the viral computational examples is given in two tarballs (TilingPrimers10kb.tar.gz, TilingPrimers3kb.tar.gz) containing subdirectories for each viral group, with text files containing the primers in fasta format and predicted hits in tab delimited text. The Supplementary information word document contains a detailed explanation of the output format of files provided in the tarballs, a listing of the MHV genomes and the regions file used in the MHV example, Table S1 containing the primers used for MHV-1 amplification, Table S2 with the primers, predicted product sizes, and PCR results used in the semi-nested PCR evaluation, and Figure S1 with the gel banding patterns from the multiplex amplification of MHV-1.

  1. Supplementary Material