Hyejin Yoon1, Thomas Leitner1. 1. Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
Abstract
SUMMARY: Analyses of entire viral genomes or mtDNA requires comprehensive design of many primers across their genomes. Furthermore, simultaneous optimization of several DNA primer design criteria may improve overall experimental efficiency and downstream bioinformatic processing. To achieve these goals, we developed PrimerDesign-M. It includes several options for multiple-primer design, allowing researchers to efficiently design walking primers that cover long DNA targets, such as entire HIV-1 genomes, and that optimizes primers simultaneously informed by genetic diversity in multiple alignments and experimental design constraints given by the user. PrimerDesign-M can also design primers that include DNA barcodes and minimize primer dimerization. PrimerDesign-M finds optimal primers for highly variable DNA targets and facilitates design flexibility by suggesting alternative designs to adapt to experimental conditions. AVAILABILITY AND IMPLEMENTATION: PrimerDesign-M is available as a webtool at http://www.hiv.lanl.gov/content/sequence/PRIMER_DESIGN/primer_design.html CONTACT: tkl@lanl.gov or seq-info@lanl.gov. Published by Oxford University Press 2014. This work is written by US Government employees and is in the public domain in the US.
SUMMARY: Analyses of entire viral genomes or mtDNA requires comprehensive design of many primers across their genomes. Furthermore, simultaneous optimization of several DNA primer design criteria may improve overall experimental efficiency and downstream bioinformatic processing. To achieve these goals, we developed PrimerDesign-M. It includes several options for multiple-primer design, allowing researchers to efficiently design walking primers that cover long DNA targets, such as entire HIV-1 genomes, and that optimizes primers simultaneously informed by genetic diversity in multiple alignments and experimental design constraints given by the user. PrimerDesign-M can also design primers that include DNA barcodes and minimize primer dimerization. PrimerDesign-M finds optimal primers for highly variable DNA targets and facilitates design flexibility by suggesting alternative designs to adapt to experimental conditions. AVAILABILITY AND IMPLEMENTATION: PrimerDesign-M is available as a webtool at http://www.hiv.lanl.gov/content/sequence/PRIMER_DESIGN/primer_design.html CONTACT: tkl@lanl.gov or seq-info@lanl.gov. Published by Oxford University Press 2014. This work is written by US Government employees and is in the public domain in the US.
Authors: Will Fischer; Vitaly V Ganusov; Elena E Giorgi; Peter T Hraber; Brandon F Keele; Thomas Leitner; Cliff S Han; Cheryl D Gleasner; Lance Green; Chien-Chi Lo; Ambarish Nag; Timothy C Wallstrom; Shuyi Wang; Andrew J McMichael; Barton F Haynes; Beatrice H Hahn; Alan S Perelson; Persephone Borrow; George M Shaw; Tanmoy Bhattacharya; Bette T Korber Journal: PLoS One Date: 2010-08-20 Impact factor: 3.240
Authors: Jakob Fredslund; Lene H Madsen; Birgit K Hougaard; Anna Marie Nielsen; David Bertioli; Niels Sandal; Jens Stougaard; Leif Schauser Journal: BMC Genomics Date: 2006-08-14 Impact factor: 3.969