Mfold protocols

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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 in pipelines

PMCID: 5871876
PMID: 29593233
DOI: 10.1038/s41598-018-23730-7

[…] control by the 1b-vdac 5′ utr, we performed a bioinformatic analysis. preliminarily, rna sequences for 1a-vdac (flybase id fbtr0332029) and 1b-vdac (flybase id fbtr0080183) were submitted to the mfold web server (at for prediction of rna secondary structure. a similar pattern of secondary structures with comparable hybridisation energies was obtained […]

PMCID: 5093897
PMID: 27808108
DOI: 10.1038/srep35962

[…] or “breeding values” of minority variants. genomic selection approaches for the isolation of high-fitness minority mutants may be extrapolated to other challenging slow growing agents., the mfold algorithm available at the mfold web server ( was used to estimate the secondary structures of the haplotype-derived ires. covariant mutations and single/double […]

PMCID: 4254888
PMID: 25512885
DOI: 10.1186/2193-1801-3-684

[…] option of the freiburg rna tools pipeline ( (will et al. , will et al. and smith et al. ), and the rna folding form option of the mfold webserver using default conditions for temperature (37°c) and ionic conditions ( (zuker ; markham and zuker ). consensus secondary structures for its1, 5.8s […]

PMCID: 4263765
PMID: 25503469
DOI: 10.1371/journal.ppat.1004553

[…] rna was examined by northern-blot hybridization every three months., the secondary structures with minimum free energy for glvd and ahvd-like rna were predicted by the circular version of the mfold program . the obtained secondary structures were further edited for print by rnaviz 2 . to search for possible kissing-loops in ahvd-like rna, the kinefold web server was used with default […]

PMCID: 3623918
PMID: 23593343
DOI: 10.1371/journal.pone.0060891

[…] etc.); brugia malayi (h30951, etc.), and meloidogyne arenaria (u42342) and aligned together with rn_var1 and rn_var2 sequences. the secondary structures of hairpin 17 were then analyzed using the mfold program with set parameters., the rn variants were also used in performing blasts searches (blastn) against unassembled reniform genomic sequences (). whole genome amplification (wga) […]

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Mfold in publications

PMCID: 5943514
PMID: 29743536
DOI: 10.1038/s41598-018-25765-2

[…] a subsequent cleavage occurred in the nascent ssrna. thus, we examined 12-nt-long ssrna oligonucleotides from the mil-682–93 and 7-nt-long mil-682–88 ssrna (fig. ). using the rna folding software mfold, we confirmed that the mil-682–93 and mil-682–88 sequences did not show base pairing interactions at room temperature; thus, they do not fold into stable secondary structures. we noticed […]

PMCID: 5940787
PMID: 29739980
DOI: 10.1038/s41598-018-25315-w

[…] small rnas were mapped to s. miltiorrhiza 99-3 genome using bowtie. no mismatch was allowed. secondary structures of genomic sequences surrounding small rna-aligned regions were predicted on the mfold web server. the structures were manually checked and mirnas were annotated under the criteria described., roots, stems, leaves and flowers of two-year-old s. miltiorrhiza were used […]

PMCID: 5936033
PMID: 29728113
DOI: 10.1186/s12917-018-1465-5

[…] of the cav genome. actually, circular ssdna is prone to forming secondary structures with a high probability. this possibility was examined and confirmed with a computational prediction from the mfold program ( (additional file : figure s1a, b). similarly, linear ssdna also has a high probability for forming secondary dna structures […]

PMCID: 5934816
PMID: 29724225
DOI: 10.1186/s12936-018-2336-z

[…] confocal microscopy)., preliminary identification and comparison of secondary structures of the aptamer sequences identified for both rpfldh- and ldhp-targeting sequences was performed using the mfold server (; []). to maintain parity with the selex conditions, structure prediction was conducted using the following environmental […]

PMCID: 5934368
PMID: 29725066
DOI: 10.1038/s41598-018-25270-6

[…] the synthetic scaffold hybridized to the two aptamer domains and run until equilibrium is reached. in this state, one can observe the reconstructed aptamer (fig. ) which agrees partially with the mfold prediction (the main discrepancy being absence of bulge and internal loops)., furthermore, to test the aptamer system integrated into the rna origami, we constructed a 212 nt long dbs scaffold […]

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

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