PrimerDesign-M: A multiple-alignment based multiple-primer design tool for walking across variable genomes
- Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
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.
- Research Organization:
- Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
- Sponsoring Organization:
- USDOE
- Grant/Contract Number:
- AC52-06NA25396
- OSTI ID:
- 1234421
- Report Number(s):
- LA-UR-14-29590
- Journal Information:
- Bioinformatics, Vol. 31, Issue 9; ISSN 1367-4803
- Country of Publication:
- United States
- Language:
- English
Web of Science
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