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Protocols

MFEprimer specifications

Information


Unique identifier OMICS_02355
Name MFEprimer
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages Python, Shell (Bash)
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Chenggang Zhang

Publications for MFEprimer

MFEprimer citations

 (20)
library_books

Taxonomy of anaerobic digestion microbiome reveals biases associated with the applied high throughput sequencing strategies

2018
Sci Rep
PMCID: 5792648
PMID: 29386622
DOI: 10.1038/s41598-018-20414-0

[…] ned from RNAmmer (v1.2) software. Sequences including the V4 region were recovered by considering the start/end positions of the alignment on hidden markov models. A “virtual PCR” was performed using MFEprimer-2.0 in order to verify the ability of universal primers to match each sequence. MFEprimer-2.0 software was launched on each 16S rRNA sequence using an automated pipeline which also parsed an […]

call_split

Ginkgolic acids inhibit migration in breast cancer cells by inhibition of NEMO sumoylation and NF κB activity

2017
Oncotarget
PMCID: 5471038
PMID: 28402272
DOI: 10.18632/oncotarget.16626
call_split See protocol

[…] Primers for uPA, PAI-1, CXCR4 and MMP-9 were designed using Primer3 (http://bioinfo.ut.ee/primer3-0.4.0/primer3/). The MFEprimer-2.0 online tool (http://biocompute.bmi.ac.cn/CZlab/MFEprimer-2.0/) was used to test primer specificity and usability. Amplification specificities were rechecked with Primer Blast (http://www […]

call_split

The ability of human nuclear DNA to cause false positive low abundance heteroplasmy calls varies across the mitochondrial genome

2016
BMC Genomics
PMCID: 5153897
PMID: 27955616
DOI: 10.1186/s12864-016-3375-x
call_split See protocol

[…] f the mitochondrial genome, were selected from regions with the lowest similarity to the nuclear genome using the proposed interference maps. Primer validation was performed using in-silico PCR using MFEprimer-3.0 []. The same software has been used to evaluate the primers employed by Li et al. []. Both specific and non-specific amplification was predicted for all primers using the human reference […]

library_books

Genome wide analysis of alternative splicing during human heart development

2016
Sci Rep
PMCID: 5067579
PMID: 27752099
DOI: 10.1038/srep35520

[…] ycles at 95 °C for 5 s, 60 °C for 1 min, cooling at 50 °C for 30 s. At the end of the qPCR runs, a melting curve was created. The primers were designed and verified using the primer 3, Oligo 7.0, and MFEprimer-2.0. The primers used in this study are shown in , and each sample was tested in triplicate. The mRNA level was normalised to glyceraldehyde 3-phosphate dehydrogenase (GAPDH), and the relati […]

call_split

Cnbp ameliorates Treacher Collins Syndrome craniofacial anomalies through a pathway that involves redox responsive genes

2016
PMCID: 5133970
PMID: 27711076
DOI: 10.1038/cddis.2016.299
call_split See protocol

[…] cleotide primers for each gene under study were designed using Primer-BLAST (http://www.ncbi.nlm.nih.gov/tools/primer-blast/) and their specificity checked using MFE http://biocompute.bmi.ac.cn/CZlab/MFEprimer-2.0/. […]

library_books

Tissue Specific Expression Patterns of MicroRNA during Acute Graft versus Host Disease in the Rat

2016
Front Immunol
PMCID: 5025478
PMID: 27695455
DOI: 10.3389/fimmu.2016.00361

[…] °C (1 min). Melting curve analysis was performed at 95°C (15 s) followed by 60°C (20 s) and 95°C (20 s). Primers were designed using NCBI PrimerBlast, and specificity was tested in silico by BLAST or MFEprimer-2.0. Primers are listed in Table . mRNA expression levels were normalized with respect to β-2-microglobulin (B2m). B2m was chosen as the preferred reference gene due to its stable expression […]

Citations

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MFEprimer institution(s)
Beijing Institute of Radiation Medicine, State Key Laboratory of Proteomics, Cognitive and Mental Health Research Center, Beijing, China; College of Life Science, Sichuan University, Key Laboratory of Bio-Resources and Eco-Environment of MOE, Chengdu, China; Beijing Institute of Health Service and Medical Information, Beijing, China
MFEprimer funding source(s)
Supported by the National Basic Research Project (973 program) [2012CB518200]; General Program [30900862, 30973107, 81070741, 81172770] of the Natural Science Foundation of China; State Key Laboratory of Proteomics of China [SKLP-O201104, SKLP-K201004, SKLP-O201002]; and Special Key Programs for Science and Technology of China [2012ZX09102301-016].

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