ArticleBMC bioinformatics2005
MPrime: efficient large scale multiple primer and oligonucleotide design for customized gene microarrays.
Article in BMC bioinformatics, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 21 citations in OpenAlex.
- BOND: Basic OligoNucleotide Design.BMC bioinformatics · 2013Article
- Flexible and efficient genome tiling design with penalized uniqueness score.BMC bioinformatics · 2012Article
- PrimerCE: designing primers for cloning and gene expression.Molecular biotechnology · 2010Article
- Database of exact tandem repeats in the Zebrafish genome.BMC genomics · 2010Article
- PrimerBank: a resource of human and mouse PCR primer pairs for gene expression detection and quantification.Nucleic acids research · 2010Article
- An evaluation of custom microarray applications: the oligonucleotide design challenge.Nucleic acids research · 2009Article
- Identification of SNPs and INDELS in swine transcribed sequences using short oligonucleotide microarrays.BMC genomics · 2008Article
- PrimerStation: a highly specific multiplex genomic PCR primer design server for the human genome.Nucleic acids research · 2006Article
- GENOMEMASKER package for designing unique genomic PCR primers.BMC bioinformatics · 2006Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundEnhancements in sequencing technology have recently yielded assemblies of large genomes including rat, mouse, human, fruit fly, and zebrafish. The availability of large-scale genomic and genic sequence data coupled with advances in microarray technology have made it possible to study the expression of large numbers of sequence products under several different conditions in days where traditional molecular biology techniques might have taken months, or even years. Therefore, to efficiently study a number of gene products associated with a disease, pathway, or other biological process, it is necessary to be able to design primer pairs or oligonucleotides en masse rather than using a time consuming and laborious gene-by-gene method.
resultsWe have developed an integrated system, MPrime, in order to efficiently calculate primer pairs or specific oligonucleotides for multiple genic regions based on a keyword, gene name, accession number, or sequence fasta format within the rat, mouse, human, fruit fly, and zebrafish genomes. A set of products created for mouse housekeeping genes from MPrime-designed primer pairs has been validated using both PCR-amplification and DNA sequencing.
conclusionThese results indicate MPrime accurately incorporates standard PCR primer design characteristics to produce high scoring primer pairs for genes of interest. In addition, sequence similarity for a set of oligonucleotides constructed for the same set of genes indicates high specificity in oligo design.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.