PrimerDesign-M: A multiple-alignment based multiple-primer design tool for walking across variable genomes
Abstract
Analyses of entire viral genomes or mtDNA requires comprehensive design of many primers across their genomes. In addition, 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.
- Authors:
-
- Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
- Publication Date:
- Research Org.:
- Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1234421
- Report Number(s):
- LA-UR-14-29590
Journal ID: ISSN 1367-4803
- Grant/Contract Number:
- AC52-06NA25396
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Bioinformatics
- Additional Journal Information:
- Journal Volume: 31; Journal Issue: 9; Journal ID: ISSN 1367-4803
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 97 MATHEMATICS AND COMPUTING
Citation Formats
Yoon, Hyejin, and Leitner, Thomas. PrimerDesign-M: A multiple-alignment based multiple-primer design tool for walking across variable genomes. United States: N. p., 2014.
Web. doi:10.1093/bioinformatics/btu832.
Yoon, Hyejin, & Leitner, Thomas. PrimerDesign-M: A multiple-alignment based multiple-primer design tool for walking across variable genomes. United States. https://doi.org/10.1093/bioinformatics/btu832
Yoon, Hyejin, and Leitner, Thomas. Wed .
"PrimerDesign-M: A multiple-alignment based multiple-primer design tool for walking across variable genomes". United States. https://doi.org/10.1093/bioinformatics/btu832. https://www.osti.gov/servlets/purl/1234421.
@article{osti_1234421,
title = {PrimerDesign-M: A multiple-alignment based multiple-primer design tool for walking across variable genomes},
author = {Yoon, Hyejin and Leitner, Thomas},
abstractNote = {Analyses of entire viral genomes or mtDNA requires comprehensive design of many primers across their genomes. In addition, 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.},
doi = {10.1093/bioinformatics/btu832},
journal = {Bioinformatics},
number = 9,
volume = 31,
place = {United States},
year = {Wed Dec 17 00:00:00 EST 2014},
month = {Wed Dec 17 00:00:00 EST 2014}
}
Web of Science
Works referenced in this record:
A multiple-alignment based primer design algorithm for genetically highly variable DNA targets
journal, January 2013
- Brodin, Johanna; Krishnamoorthy, Mohan; Athreya, Gayathri
- BMC Bioinformatics, Vol. 14, Issue 1
Quantitative experimental determination of primer-dimer formation risk by free-solution conjugate electrophoresis
journal, January 2012
- Desmarais, Samantha M.; Leitner, Thomas; Barron, Annelise E.
- ELECTROPHORESIS, Vol. 33, Issue 3
Transmission of Single HIV-1 Genomes and Dynamics of Early Immune Escape Revealed by Ultra-Deep Sequencing
journal, August 2010
- Fischer, Will; Ganusov, Vitaly V.; Giorgi, Elena E.
- PLoS ONE, Vol. 5, Issue 8
A general pipeline for the development of anchor markers for comparative genomics in plants
journal, August 2006
- Fredslund, Jakob; Madsen, Lene H.; Hougaard, Birgit K.
- BMC Genomics, Vol. 7, Issue 1
Java web tools for PCR, in silico PCR, and oligonucleotide assembly and analysis
journal, August 2011
- Kalendar, Ruslan; Lee, David; Schulman, Alan H.
- Genomics, Vol. 98, Issue 2
OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach
journal, June 2003
- Rouillard, J. -M.
- Nucleic Acids Research, Vol. 31, Issue 12
Improved Nearest-Neighbor Parameters for Predicting DNA Duplex Stability †
journal, January 1996
- SantaLucia,, John; Allawi, Hatim T.; Seneviratne, P. Ananda
- Biochemistry, Vol. 35, Issue 11
Primer3—new capabilities and interfaces
journal, June 2012
- Untergasser, Andreas; Cutcutache, Ioana; Koressaar, Triinu
- Nucleic Acids Research, Vol. 40, Issue 15
SNPbox: a modular software package for large-scale primer design
journal, September 2004
- Weckx, S.; De Rijk, P.; Van Broeckhoven, C.
- Bioinformatics, Vol. 21, Issue 3
Works referencing / citing this record:
Characterization and mutagenesis of Chinese hamster ovary cells endogenous retroviruses to inactivate viral particle release
journal, November 2019
- Duroy, Pierre‐Olivier; Bosshard, Sandra; Schmid‐Siegert, Emanuel
- Biotechnology and Bioengineering, Vol. 117, Issue 2
Evolution of nickel hyperaccumulation and serpentine adaptation in the Alyssum serpyllifolium species complex
journal, October 2016
- Sobczyk, M. K.; Smith, J. A. C.; Pollard, A. J.
- Heredity, Vol. 118, Issue 1
Bovine viral diarrhoea virus loses quasispecies diversity rapidly in culture
posted_content, January 2020
- Russell, George C.; Zadoks, Ruth N.; Willoughby, Kim
- bioRxiv
discomark : nuclear marker discovery from orthologous sequences using draft genome data
journal, August 2016
- Rutschmann, Sereina; Detering, Harald; Simon, Sabrina
- Molecular Ecology Resources, Vol. 17, Issue 2
Redefinition and Unification of the SXT/R391 Family of Integrative and Conjugative Elements
journal, April 2018
- Bioteau, Audrey; Durand, Romain; Burrus, Vincent
- Applied and Environmental Microbiology, Vol. 84, Issue 13
Bovine viral diarrhoea virus loses quasispecies diversity rapidly in culture
journal, April 2020
- Russell, George C.; Zadoks, Ruth N.; Willoughby, Kim
- Microbial Genomics, Vol. 6, Issue 4
DiscoMark: Nuclear marker discovery from orthologous sequences using draft genome data
journal, July 2016
- Rutschmann, Sereina; Detering, Harald; Simon, Sabrina
- Molecular Ecology Resources
Bovine viral diarrhoea virus loses quasispecies diversity rapidly in culture
text, January 2020
- Russell, George C.; Zadoks, Ruth N.; Willoughby, Kim
- Society for General Microbiology
Characterization and mutagenesis of Chinese hamster ovary cells endogenous retroviruses to inactivate viral particle release
journal, November 2019
- Duroy, Pierre‐Olivier; Bosshard, Sandra; Schmid‐Siegert, Emanuel
- Biotechnology and Bioengineering, Vol. 117, Issue 2
PrimerMapper: high throughput primer design and graphical assembly for PCR and SNP detection
journal, February 2016
- O’Halloran, Damien M.
- Scientific Reports, Vol. 6, Issue 1
ZikaVR: An Integrated Zika Virus Resource for Genomics, Proteomics, Phylogenetic and Therapeutic Analysis
journal, September 2016
- Gupta, Amit Kumar; Kaur, Karambir; Rajput, Akanksha
- Scientific Reports, Vol. 6, Issue 1
NipahVR: a resource of multi-targeted putative therapeutics and epitopes for the Nipah virus
journal, January 2020
- Gupta, Amit Kumar; Kumar, Archit; Rajput, Akanksha
- Database, Vol. 2020