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. 2011 Jan 15;27(2):266-7.
doi: 10.1093/bioinformatics/btq624. Epub 2010 Nov 9.

PriSM: a primer selection and matching tool for amplification and sequencing of viral genomes

Qing Yu  1 , Elizabeth M Ryan, Todd M Allen, Bruce W Birren, Matthew R Henn, Niall J Lennon
Affiliations

PriSM: a primer selection and matching tool for amplification and sequencing of viral genomes

Qing Yu et al. Bioinformatics. .

Abstract

Summary: 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.

Availability: The program is freely available for use at: www.broadinstitute.org/perl/seq/specialprojects/primerDesign.cgi.

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References

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