Mfold

Mfold web server for nucleic acid folding and hybridization prediction. The abbreviated name, ‘mfold web server’, describes a number of closely related software applications available on the World Wide Web (WWW) for the prediction of the secondary structure of single stranded nucleic acids. The objective of this web server is to provide easy access to RNA and DNA folding and hybridization software to the scientific community at large. By making use of universally available web GUIs (Graphical User Interfaces), the server circumvents the problem of portability of this software. Detailed output, in the form of structure plots with or without reliability information, single strand frequency plots and ‘energy dot plots’, are available for the folding of single sequences. A variety of ‘bulk’ servers give less information, but in a shorter time and for up to hundreds of sequences at once. The portal for the mfold web server is http://www.bioinfo.rpi.edu/applications/mfold. This URL will be referred to as ‘MFOLDROOT’.


References in zbMATH (referenced in 25 articles )

Showing results 1 to 20 of 25.
Sorted by year (citations)

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  1. Jin, Emma Yu; Nebel, Markus E.: RNA secondary structures in a polymer-zeta model how foldings should be shaped for sparsification to establish a linear speedup (2016)
  2. Picardi, Ernesto (ed.): RNA bioinformatics (2015)
  3. Bundschuh, Ralf: Unified approach to partition functions of RNA secondary structures (2014)
  4. Fusy, Éric; Clote, Peter: Combinatorics of locally optimal RNA secondary structures (2014)
  5. Clote, Peter; Kranakis, Evangelos; Krizanc, Danny: Asymptotic number of hairpins of saturated RNA secondary structures (2013)
  6. Clote, Peter; Dobrev, Stefan; Dotu, Ivan; Kranakis, Evangelos; Krizanc, Danny; Urrutia, Jorge: On the page number of RNA secondary structures with pseudoknots (2012)
  7. Clote, Peter; Ponty, Yann; Steyaert, Jean-Marc: Expected distance between terminal nucleotides of RNA secondary structures (2012)
  8. Backofen, Rolf; Tsur, Dekel; Zakov, Shay; Ziv-Ukelson, Michal: Sparse RNA folding: time and space efficient algorithms (2011)
  9. Hower, Valerie; Heitsch, Christine E.: Parametric analysis of RNA branching configurations (2011)
  10. Baev, Vesselin; Daskalova, Evelina; Minkov, Ivan: Computational identification of novel microRNA homologs in the chimpanzee genome (2009)
  11. Bakhtin, Yuri; Heitsch, Christine E.: Large deviations for random trees and the branching of RNA secondary structures (2009)
  12. Kato, Yuki; Akutsu, Tatsuya; Seki, Hiroyuki: A grammatical approach to RNA-RNA interaction prediction (2009)
  13. Zhang, Wenwei; Luo, Yuping; Gong, Xi; Zeng, Wenhong; Li, Siguangc: Computational identification of 48 potato microRNAs and their targets (2009)
  14. Chan, Chi Yu; Ding, Ye: Boltzmann ensemble features of RNA secondary structures: a comparative analysis of biological RNA sequences and random shuffles (2008)
  15. Clote, Peter: Introduction to special issue on RNA (2008)
  16. Khaladkar, Mugdha; Patel, Vandanaben; Bellofatto, Vivian; Wilusz, Jeffrey; Wang, Jason T.L.: Detecting conserved secondary structures in RNA molecules using constrained structural alignment (2008)
  17. Machado-Lima, Ariane; del Portillo, Hernando A.; Durham, Alan Mitchell: Computational methods in noncoding RNA research (2008)
  18. Zamorano, Absalom; López-Camarillo, César; Orozco, Esther; Weber, Christian; Guillen, Nancy; Marchat, Laurence A.: In silico analysis of EST and genomic sequences allowed the prediction of cis-regulatory elements for Entamoeba histolytica mRNA polyadenylation (2008)
  19. Jin, Wei-Bo; Wu, Fang-Li; Kong, Dong; Guo, Ai-Guang: HBV-encoded microRNA candidate and its target (2007)
  20. Prohaska, Sonja J.; Mosig, Axel; Stadler, Peter F.: Regulatory signals in genomic sequences (2007)

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Further publications can be found at: http://mfold.rit.albany.edu/?q=mfold/mfold-references