Assessing primer specificity and predicting both desired and off-target amplification products is an essential step for robust PCR assay design. This script predicts potential polymerase chain reaction (PCR) amplicons in a large sequence database such as NCBI nt from either singleplex or a large multiplexed set of primers, allowing degenerate primer and probe bases, with target mismatch tolerance and amplicon length range to be set by the user. The PCR amplicon simulation code also annotates amplicons with gene information automatically downloaded from NCBI, and optionally it can predict whether there are also TaqMan/Luminex probe matches within predicted amplicons. It is an open source command line Perl script called simulate_PCR.pl that calls the BLAST (Altschul, et al., 1990) programs makeblastdb, blastn, and blastdbcmd, and the NCBI efetch utility (http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi).

Project Activity

See All Activity >

Follow simulate_pcr

simulate_pcr Web Site

Other Useful Business Software
Enterprise-grade ITSM, for every business Icon
Enterprise-grade ITSM, for every business

Give your IT, operations, and business teams the ability to deliver exceptional services—without the complexity.

Freshservice is an intuitive, AI-powered platform that helps IT, operations, and business teams deliver exceptional service without the usual complexity. Automate repetitive tasks, resolve issues faster, and provide seamless support across the organization. From managing incidents and assets to driving smarter decisions, Freshservice makes it easy to stay efficient and scale with confidence.
Try it Free
Rate This Project
Login To Rate This Project

User Reviews

Be the first to post a review of simulate_pcr!

Additional Project Details

Registered

2013-09-05