ArticleNucleic acids research2001
GST-PRIME: a genome-wide primer design software for the generation of gene sequence tags.
Article in Nucleic acids research, 2001. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed, 27 citations in OpenAlex.
- Developing nucleic acid-based electrical detection systems.Microbial cell factories · 2006Article
- MPrime: efficient large scale multiple primer and oligonucleotide design for customized gene microarrays.BMC bioinformatics · 2005Article
- Versatile gene-specific sequence tags for Arabidopsis functional genomics: transcript profiling and reverse genetics applications.Genome research · 2004Article
- Genome-scale design of PCR primers and long oligomers for DNA microarrays.Nucleic acids research · 2003Article
- Regionalized GC content of template DNA as a predictor of PCR success.Nucleic acids research · 2003Article
- The Arabidopsis ppi1 mutant is specifically defective in the expression, chloroplast import, and accumulation of photosynthetic proteins.The Plant cell · 2003Article
- Covariations in the nuclear chloroplast transcriptome reveal a regulatory master-switch.EMBO reports · 2003Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The availability of sequenced genomes has generated a need for experimental approaches that allow the simultaneous analysis of large, or even complete, sets of genes. To facilitate such analyses, we have developed GST-PRIME, a software package for retrieving and assembling gene sequences, even from complex genomes, using the NCBI public database, and then designing sets of primer pairs for use in gene amplification. Primers were designed by the program for the direct amplification of gene sequence tags (GSTs) from either genomic DNA or cDNA. Test runs of GST-PRIME on 2000 randomly selected Arabidopsis and Drosophila genes demonstrate that 93 and 88% of resulting GSTs, respectively, fulfilled imposed length criteria. GST-PRIME primer pairs were tested on a set of 1900 Arabidopsis genes coding for chloroplast-targeted proteins: 95% of the primer pairs used in PCRs with genomic DNA generated the correct amplicons. GST-PRIME can thus be reliably used for large-scale or specific amplification of intron-containing genes of multicellular eukaryotes.
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