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Protocols

UNAFold specifications

Information


Unique identifier OMICS_04461
Name UNAFold
Alternative name Unified Nucleic Acid Folding
Interface Web user interface
Restrictions to use None
Input data A sequence.
Computer skills Basic
Stability Stable
Maintained Yes

Information


Unique identifier OMICS_04461
Name UNAFold
Alternative name Unified Nucleic Acid Folding
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Perl
Computer skills Advanced
Version 3.9
Maintained Yes

Versioning


No version available

Publications for Unified Nucleic Acid Folding

UNAFold citations

 (103)
library_books

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

2018
Sci Rep
PMCID: 5954100
PMID: 29765106
DOI: 10.1038/s41598-018-25981-w

[…] ultiple 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 (http://unafold.rna.albany.edu/?q=mfold/DNA-Folding-Form).To extend the tRNA-predictions provided by MITOS with the MiTFi approach, we also applied the MITOS2 webserver (revision 941; http://mitos2.bioinf.uni […]

call_split

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

2018
BMC Genomics
PMCID: 5896051
PMID: 29642859
DOI: 10.1186/s12864-018-4608-y
call_split See protocol

[…] formed using MUSTv2 software [] (http://www.healthinformaticslab.org/supp/resources.php). Predicted RNA secondary structures used to confirm the presence of TIRs were generated using mfold [] (http://unafold.rna.albany.edu/?q=mfold). In order to demonstrate the potential for transcription of QMITE inserts, prediction of sigma-70 consensus promoter elements and Rho factor-independent terminators in […]

library_books

Targeting the polyadenylation factor EhCFIm25 with RNA aptamers controls survival in Entamoeba histolytica

2018
Sci Rep
PMCID: 5890266
PMID: 29632392
DOI: 10.1038/s41598-018-23997-w

[…] The secondary structure of C4 and C5 aptamers was predicted using the Unified Nucleic Acid Folding and hybridization package (http://unafold.rna.albany.edu/),. The three-dimensional structure of EhCFIm25 (C4M2T1, 255 residues) was predicted by homology modeling with the […]

library_books

Phylogenomic and comparative analysis of the distribution and regulatory patterns of TPP riboswitches in fungi

2018
Sci Rep
PMCID: 5882874
PMID: 29615754
DOI: 10.1038/s41598-018-23900-7

[…] ns which generate the optimal and sub-optimal secondary structures for the potential riboswitch candidates. These folding predictions obtained on the basis of energy minimization can be computed with UNAFold or the Vienna RNA package and can be compared to the reference riboswitch structure derived by comparative analysis or x-ray crystallography/NMR experiment. We chose to work with UNAFold for f […]

library_books

Mechanism of translation control of the alternative Drosophila melanogaster Voltage Dependent Anion selective Channel 1 mRNAs

2018
Sci Rep
PMCID: 5871876
PMID: 29593233
DOI: 10.1038/s41598-018-23730-7

[…] 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 http://unafold.rna.albany.edu) for prediction of RNA secondary structure. A similar pattern of secondary structures with comparable hybridisation energies was obtained for both D. melanogaster VDAC mRNAs.Fur […]

library_books

Evolution of echovirus 11 in a chronically infected immunodeficient patient

2018
PLoS Pathog
PMCID: 5875893
PMID: 29554133
DOI: 10.1371/journal.ppat.1006943

[…] ng the Sequencher v5.2.2 program (Gencodes, Anne Arbor, MI, USAS).Three-dimensional folding models of Loop V of the internal ribosomal entry site (IRES) in the 5’UTR were prepared using the web-based Unified Nucleic Acid Folding and hybridizing Package [, ] at the University of Albany NY, USA, (http://mfold.rna.albany.edu; last accessed November 2014) and the consensus sequence for the Israeli iso […]

Citations

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UNAFold institution(s)
Xerox Litigation Services, Albany, NY, USA

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