PriSM: a primer selection and matching tool for amplification and sequencing of viral genomes.
CONCLUSIONS
PriSM is a set of algorithms designed to select and match degenerate primer pairs for the amplification of viral genomes. The design of panels of hundreds of primer pairs takes just hours using this program, compared with days using a manual approach. PriSM allows for rapid in silico optimization of primers for downstream applications such as sequencing. As a validation, PriSM was used to create an amplification primer panel for human immunodeficiency virus (HIV) Clade B.


BACKGROUND
The program is freely available for use at: www.broadinstitute.org/perl/seq/specialprojects/primerDesign.cgi.
Broad Institute of MIT & Harvard, Cambridge, MA 02142, USA.
Qing
Q
Yu
Elizabeth M
EM
Ryan
Todd M
TM
Allen
Bruce W
BW
Birren
Matthew R
MR
Henn
Niall J
NJ
Lennon
D000465:Algorithms; D017931:DNA Primers / Q000737:chemistry*; D016679:Genome, Viral; D006678:HIV / Q000235:genetics; D006801:Humans; D016133:Polymerase Chain Reaction; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA; D012984:Software
D017931:DNA Primers