DINAMelt statistics

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Number of citations per year for the bioinformatics software tool DINAMelt
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Protocols

DINAMelt specifications

Information


Unique identifier OMICS_25243
Name DINAMelt
Interface Web user interface
Restrictions to use None
Input data Two sequences.
Output data A form, several plots and several text files containing thermodynamic data that can be downloaded in a single file.
Output format ZIP
Computer skills Basic
Maintained Yes

Maintainer


  • person_outline Michael Zuker

Publication for DINAMelt

DINAMelt citations

 (19)
call_split

Genome wide Identification and Characterization of Natural Antisense Transcripts by Strand specific RNA Sequencing in Ganoderma lucidum

2017
Sci Rep
PMCID: 5515960
PMID: 28720793
DOI: 10.1038/s41598-017-04303-6
call_split See protocol

[…] pt, they were classified as ‘high-coverage’. In step 2, the trans-SAT pairs obtained from step 1 were examined to determine if they could melt into RNA–RNA duplexes in the complementary regions using DINAMelt. In step 3, if the annealed region identified by DINAMelt coincided with the BLASTN results, and if any bubble within the annealed region had a length not longer than 10% of the region’s leng […]

library_books

Genetic Predisposition To Acquire a Polybasic Cleavage Site for Highly Pathogenic Avian Influenza Virus Hemagglutinin

2017
MBio
PMCID: 5312086
PMID: 28196963
DOI: 10.1128/mBio.02298-16

[…] The Quickfold program (http://unafold.rna.albany.edu/?q=DINAMelt/Quickfold) () and RNAfold program from the ViennaRNA Web Services (http://rna.tbi.univie.ac.at/) and the ViennaRNA package () were used to predict the secondary structures of the RNAseqHAclv […]

library_books

Things Are Getting Hairy: Enterobacteria Bacteriophage vB_PcaM_CBB

2017
Front Microbiol
PMCID: 5259590
PMID: 28174560
DOI: 10.3389/fmicb.2017.00044

[…] e located with ARNOLD (http://rna.igmors.u-psud.fr/toolbox/arnold/; Naville et al., ) with predictions being verified using Mfold Quikfold using RNA energy rules 3.0 (http://unafold.rna.albany.edu/?q=DINAMelt/Quickfold; Zuker, ). Codon usage of CBB was analyzed using University of Georgia's amino acid and codon usage statistics services (http://www.cmbl.uga.edu/software/codon_usage.html).Coregenes […]

library_books

DyNAMiC Workbench: an integrated development environment for dynamic DNA nanotechnology

2015
PMCID: 4614494
PMID: 26423437
DOI: 10.1098/rsif.2015.0580

[…] egrates directly with several publicly available Web services for sequence-level analysis. The NUPACK Web server can perform full partition function and pair probability calculation []. The Mfold and DINAmelt Web servers provide several types of analysis [,]. The TBI Vienna RNAfold Web server allows computation of the MFE structure and partition function []. These software tools provide a wide ran […]

library_books

On the Normalization of the Minimum Free Energy of RNAs by Sequence Length

2014
PLoS One
PMCID: 4236180
PMID: 25405875
DOI: 10.1371/journal.pone.0113380

[…] MFE was computed using two programs: RNAfold, included in the ViennaRNA software package version 2.1.5 , ; and Quickfold, from the Mfold web server (http://mfold.rna.albany.edu/?q=DINAMelt/Quickfold) , . For very short sequences, we found that the MFEs computed by Quickfold (Mfold) were sometimes positive. In these cases, global free energy were set to 0 kcal/mol.AMFE was calcu […]

call_split

Nanopore Biosensor for Label Free and Real Time Detection of Anthrax Lethal Factor

2014
PMCID: 4039345
PMID: 24806593
DOI: 10.1021/am500749p
call_split See protocol

[…] dwell time histograms by fitting the distributions to single exponential functions by the Levenberg–Marquardt procedure. Thermodynamics of hairpin folding and DNA hybridization was obtained from the DINAMelt web server. […]


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DINAMelt institution(s)
Department of Computer Science, Rensselaer Polytechnic Institute, Troy, NY, USA; Department of Mathematical Sciences, Rensselaer Polytechnic Institute, Troy, NY, USA
DINAMelt funding source(s)
Supported by the National Institutes of Health and by a Graduate Fellowship from RPI.

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