title: PrimerDesign-M: a multiple-alignment based multiple-primer design tool for walking across variable genomes.
abstract: CONCLUSIONS
  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.
  
  
  METHODS
  PrimerDesign-M is available as a webtool at http://www.hiv.lanl.gov/content/sequence/PRIMER_DESIGN/primer_design.html
  
  
  BACKGROUND
  tkl@lanl.gov or seq-info@lanl.gov.
authors.affiliation: Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
authors.forename: Hyejin
authors.initials: H
authors.lastname: Yoon
authors.affiliation: Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
authors.forename: Thomas
authors.initials: T
authors.lastname: Leitner
mesh_terms: D017931:DNA Primers / Q000737:chemistry*; D016679:Genome, Viral; D023281:Genomics / Q000379:methods; D015497:HIV-1 / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D012984:Software
chemical_list: D017931:DNA Primers