Genome-scale probe and primer design with PRIMEGENS.
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/.
Srivastava
Gyan Prakash
GP
Digital BiologyLaboratory, Computer Science Department University of Missouri-Columbia, USA.
Xu
Dong
D
D000465:Algorithms; D017931:DNA Primers / Q000737:chemistry* / Q000235:genetics; D016678:Genome / Q000235:genetics; D020407:Internet; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods; D017422:Sequence Analysis, DNA; D012984:Software; D014584:User-Computer Interface
D017931:DNA Primers