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- Title
Enhancements and modifications of primer design program Primer3.
- Authors
Triinu Koressaar; Maido Remm
- Abstract
Summary: The determination of annealing temperature is a critical step in PCR design. This parameter is typically derived from the melting temperature of the PCR primers, so for successful PCR work it is important to determine the melting temperature of primer accurately. We introduced several enhancements in the widely used primer design program Primer3. The improvements include a formula for calculating melting temperature and a salt correction formula. Also, the new version can take into account the effects of divalent cations, which are included in most PCR buffers. Another modification enables using lowercase masked template sequences for primer design. Availability: Features described in this article have been implemented into the development code of Primer3 and will be available in future versions (version 1.1 and newer) of Primer3. Also, a modified version is compiled under the name of mPrimer3 which is distributed independently. The web-based version of mPrimer3 is available at http://bioinfo.ebc.ee/mprimer3/ and the binary code is freely downloadable from the URL http://bioinfo.ebc.ee/download/. Contact: maido.remm@ut.ee
- Subjects
COMPUTER software; SOFTWARE architecture; TEMPERATURE measurements; MELTING points
- Publication
Bioinformatics, 2007, Vol 23, Issue 10, p1289
- ISSN
1367-4803
- Publication type
Article
- DOI
10.1093/bioinformatics/btm091