Genome-Scale Probe and Primer Design with PRIMEGENS

Gyan Srivastava; Dong Xu

doi:10.1007/978-1-59745-528-2_8

Abstract

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/.

Keywords

Primer (cosmetics)Computational biologyScale (ratio)BiologyGeneticsGeographyPhysicsCartography

Affiliated Institutions

University of Missouri US

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Publication Info

Year: 2007
Type: review
Volume: 402
Pages: 159-175
Citations: 11
Access: Closed

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APA Style

                            
                                    Gyan Srivastava, 
                                
                                    Dong Xu
                                
                            (2007). 
                            Genome-Scale Probe and Primer Design with PRIMEGENS. 
                            Methods in molecular biology
                            , 402
                            
                            , 159-175.
                            https://doi.org/10.1007/978-1-59745-528-2_8

Identifiers

DOI: 10.1007/978-1-59745-528-2_8