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Mfold specifications


Unique identifier OMICS_04749
Name Mfold
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes


  • person_outline Michael Zuker

Publications for Mfold

Mfold citations


The mitochondrial genome of the oribatid mite Paraleius leontonychus: new insights into tRNA evolution and phylogenetic relationships in acariform mites

Sci Rep
PMCID: 5954100
PMID: 29765106
DOI: 10.1038/s41598-018-25981-w

[…] Table ) and performed a multiple sequence alignment with MUSCLE and extended the 16S gene based on the observed conserved regions. Secondary structures in the control region were identified using the Mfold web server ( extend the tRNA-predictions provided by MITOS with the MiTFi approach, we also applied the MITOS2 webserver (revision 941; […]


Nanotechnology based approaches for detection and delivery of microRNA in healthcare and crop protection

PMCID: 5897953
PMID: 29653577
DOI: 10.1186/s12951-018-0368-8

[…] folding of RNA molecules are yet to be classified. With the use of RNA 2D structure prediction programme, only 70% of structure can be predicted accurately [, ]. Though various online resources like Mfold, 233 RNA designer, 234 Sfold, 235 NUPACK, 115 nanofolder, 236 and hyperfold, 182 have been developed, prediction of accurate RNA structure and folding remains a major problem. RNA 3D and 4D stru […]


A new diatom species P. hallegraeffii sp. nov. belonging to the toxic genus Pseudo nitzschia (Bacillariophyceae) from the East Australian Current

PLoS One
PMCID: 5896966
PMID: 29649303
DOI: 10.1371/journal.pone.0195622

[…] omal termini, the annotated ITS2 sequences were aligned using ClustalW in MEGA v7 and adjusted manually. The secondary structures of the ITS2 region from P. hallegraeffii strains were predicted using Mfold using the default parameters []. RNA transcript folding of ITS2 for the two Pseudo-nitzschia strains in this study was predicted by the ITS2 Database V using default settings (http://its2.bioapp […]


Identification of novel MITEs (miniature inverted repeat transposable elements) in Coxiella burnetii: implications for protein and small RNA evolution

BMC Genomics
PMCID: 5896051
PMID: 29642859
DOI: 10.1186/s12864-018-4608-y
call_split See protocol

[…] 3 genome were performed using MUSTv2 software [] ( Predicted RNA secondary structures used to confirm the presence of TIRs were generated using mfold [] ( In order to demonstrate the potential for transcription of QMITE inserts, prediction of sigma-70 consensus promoter elements and Rho factor-independe […]


Characterization of a New Staphylococcus aureus Kayvirus Harboring a Lysin Active against Biofilms

PMCID: 5923476
PMID: 29642449
DOI: 10.3390/v10040182

[…] .Promoter regions were determined using PromoterHunter from the phiSITE database [] and checked manually. ARNold [] was used to predict rho-independent terminators and the energy was calculated using Mfold []. The DNA homology comparisons between phages were conducted with progressiveMauve [].The phylogenetic analysis of homologous phages was performed on Geneious 9.1.4. For phylogenetic purposes, […]


Intragenomic Long Distance RNA–RNA Interactions in Plus Strand RNA Plant Viruses

Front Microbiol
PMCID: 5893793
PMID: 29670583
DOI: 10.3389/fmicb.2018.00529

[…] pproaches, however, some LDRIs may be missed, and only a small subset is likely to be functional. Regardless, performing viral genome folding using RNA secondary structure predicting programs such as mFOLD can be informative regarding potential LDRIs (). Additionally, programs such as intraRNA and LRIscan designed specifically for identifying interactions based on the extent of pairing and/or the […]


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Mfold institution(s)
Department of Mathematical Sciences, Rensselaer Polytechnic Institute, Troy, NY, USA

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