ArticleNucleic acids research2003
Genome-scale design of PCR primers and long oligomers for DNA microarrays.
Article in Nucleic acids research, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Functional analysis and identification of cis-regulatory elements of human chromosome 21 gene promoters.Nucleic acids research · 2010Article
- Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments.Nucleic acids research · 2010Article
- The presence of the internalin gene in natural atypically hemolytic Listeria innocua strains suggests descent from L. monocytogenes.Applied and environmental microbiology · 2007Article
- PrimerStation: a highly specific multiplex genomic PCR primer design server for the human genome.Nucleic acids research · 2006Article
- Intracellular gene expression profile of Listeria monocytogenes.Infection and immunity · 2006Article
- Genomewide analysis of nucleosome density histone acetylation and HDAC function in fission yeast.The EMBO journal · 2005Article
- A generic approach for the design of whole-genome oligoarrays, validated for genomotyping, deletion mapping and gene expression analysis on Staphylococcus aureus.BMC genomics · 2005Article
- Strengths and weaknesses of EST-based prediction of tissue-specific alternative splicing.BMC genomics · 2004Article
- SNPbox: web-based high-throughput primer design from gene to genome.Nucleic acids research · 2004Article
- An integrated gene annotation and transcriptional profiling approach towards the full gene content of the Drosophila genome.Genome biology · 2003Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
During the last years, the demand for custom-made cDNA chips/arrays as well as whole genome chips is increasing rapidly. The efficient selection of gene-specific primers/oligomers is of the utmost importance for the successful production of such chips. We developed GenomePRIDE, a highly flexible and scalable software for designing primers/oligomers for large-scale projects. The program is able to generate either long oligomers (40-70 bases), or PCR primers for the amplification of gene-specific DNA fragments of user-defined length. Additionally, primers can be designed in-frame in order to facilitate large-scale cloning into expression vectors. Furthermore, GenomePRIDE can be adapted to specific applications such as the generation of genomic amplicon arrays or the design of fragments specific for alternative splice isoforms. We tested the performance of GenomePRIDE on the entire genomes of Listeria monocytogenes (1584 gene-specific PCRs, 48 long oligomers) as well as of eukaryotes such as Schizosaccharomyces pombe (5006 gene-specific PCRs), and Drosophila melanogaster (21 306 gene-specific PCRs). With its computing speed of 1000 primer pairs per hour and a PCR amplification success of 99%, GenomePRIDE represents an extremely cost- and time-effective program.
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