ArticleBMC bioinformatics2006
GENOMEMASKER package for designing unique genomic PCR primers.
Article in BMC bioinformatics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Identification and functional analysis of exonic SNPs in MMP2 and MMP3 genes as prognostic biomarkers for breast cancer patients.Molecular genetics and genomics : MGG · 2026Article
- Precise characterization of somatic complex structural variations from tumor/control paired long-read sequencing data with nanomonsv.Nucleic acids research · 2023Article
- Development of a genome-wide marker design workflow for onions and its application in target amplicon sequencing-based genotyping.DNA research : an international journal for rapid publication of reports on genes and genomes · 2022Article
- Genetic characterization of populations in the Marquesas Archipelago in the context of the Austronesian expansion.Scientific reports · 2022Article
- Prediction of PCR amplification from primer and template sequences using recurrent neural network.Scientific reports · 2021Article
- Soybean antiviral immunity conferred by dsRNase targets the viral replication complex.Nature communications · 2019Article
- MFEprimer-3.0: quality control for PCR primers.Nucleic acids research · 2019Article
- Y-chromosomal connection between Hungarians and geographically distant populations of the Ural Mountain region and West Siberia.Scientific reports · 2019Article
- Development of a high-density linkage map and chromosome segment substitution lines for Japanese soybean cultivar Enrei.DNA research : an international journal for rapid publication of reports on genes and genomes · 2018Article
- ThermoAlign: a genome-aware primer design tool for tiled amplicon resequencing.Scientific reports · 2017Article
- Human Y Chromosome Haplogroup N: A Non-trivial Time-Resolved Phylogeography that Cuts across Language Families.American journal of human genetics · 2016Article
- Construction of a high-density mutant library in soybean and development of a mutant retrieval method using amplicon sequencing.BMC genomics · 2015Article
- Genetic analysis of membrane cofactor protein (CD46) of the complement system in women with and without preeclamptic pregnancies.PloS one · 2015Article
- PrecisePrimer: an easy-to-use web server for designing PCR primers for DNA library cloning and DNA shuffling.Nucleic acids research · 2014Article
- Article
- Primer3--new capabilities and interfaces.Nucleic acids research · 2012Article
- MFEprimer-2.0: a fast thermodynamics-based program for checking PCR primer specificity.Nucleic acids research · 2012Article
- Evaluation of soybean germplasm conserved in NIAS genebank and development of mini core collections.Breeding science · 2012Article
- Identification of repetitive elements in the genome of Oreochromis niloticus: tilapia repeat masker.Marine biotechnology (New York, N.Y.) · 2010Article
- Development of a single tube 640-plex genotyping method for detection of nucleic acid variations on microarrays.Nucleic acids research · 2008Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe design of oligonucleotides and PCR primers for studying large genomes is complicated by the redundancy of sequences. The eukaryotic genomes are particularly difficult to study due to abundant repeats. The speed of most existing primer evaluation programs is not sufficient for large-scale experiments.
resultsIn order to improve the efficiency and success rate of automatic primer/oligo design, we created a novel method which allows rapid masking of repeats in large sequence files, for example in eukaryotic genomes. It also allows the detection of all alternative binding sites of PCR primers and the prediction of PCR products. The new method was implemented in a collection of efficient programs, the GENOMEMASKER package. The performance of the programs was compared to other similar programs. We also modified the PRIMER3 program, to be able to design primers from lowercase-masked sequences.
conclusionThe GENOMEMASKER package is able to mask the entire human genome for non-unique primers within 6 hours and find locations of all binding sites for 10,000 designed primer pairs within 10 minutes. Additionally, it predicts all alternative PCR products from large genomes for given primer pairs.
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