Summary
This chapter introduces the software package PRIMEGENS for designing gene-specific probes and associated PCR primers on a large scale. Such design is especially useful for constructing cDNA or oligo microarray to minimize cross-hybridization. PRIMEGENS can also be used for designing primers to amplify a segment of a unique target gene using reverse-transcriptase (RT)–PCR. The input to PRIMEGENS is a set of sequences, whose primers need to be designed, and a sequence pool containing all the genes in a genome. It provides options to choose various parameters. PRIMEGENS uses a systematic algorithm for designing gene-specific probes and its primer pair. For a given sequence, PRIMEGENS first searches for the longest gene-specific fragment and then designs best PCR product for this fragment. The 2.0 version of PRIMEGENS provides a graphical user interface (GUI) with additional features. The software is freely available for any users and can be downloaded from http://digbio.missouri.edu/primegens/.
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© 2007 Humana Press
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Srivastava, G.P., Xu, D. (2007). Genome-Scale Probe and Primer Design with PRIMEGENS. In: Yuryev, A. (eds) PCR Primer Design. Methods in Molecular Biology™, vol 402. Humana Press. https://doi.org/10.1007/978-1-59745-528-2_8
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DOI: https://doi.org/10.1007/978-1-59745-528-2_8
Publisher Name: Humana Press
Print ISBN: 978-1-58829-725-9
Online ISBN: 978-1-59745-528-2
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