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 39 articles )

Showing results 1 to 20 of 39.
Sorted by year (citations)

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  1. Han, Yo-Sub; Kim, Hwee: Ruleset optimization on isomorphic oritatami systems (2019)
  2. Barrera-Cruz, Fidel; Heitsch, Christine; Poznanović, Svetlana: On the structure of RNA branching polytopes (2018)
  3. Han, Yo-Sub; Kim, Hwee; Ota, Makoto; Seki, Shinnosuke: Nondeterministic seedless oritatami systems and hardness of testing their equivalence (2016)
  4. 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)
  5. Picardi, Ernesto (ed.): RNA bioinformatics (2015)
  6. Bundschuh, Ralf: Unified approach to partition functions of RNA secondary structures (2014)
  7. Fusy, Éric; Clote, Peter: Combinatorics of locally optimal RNA secondary structures (2014)
  8. Clote, Peter; Kranakis, Evangelos; Krizanc, Danny: Asymptotic number of hairpins of saturated RNA secondary structures (2013)
  9. Manzourolajdad, Amirhossein; Wang, Yingfeng; Shaw, Timothy I.; Malmberg, Russell L.: Information-theoretic uncertainty of SCFG-modeled folding space of the non-coding RNA (2013)
  10. Churkin, Alexander; Gabdank, Idan; Barash, Danny: On topological indices for small RNA graphs (2012)
  11. Clote, Peter; Dobrev, Stefan; Dotu, Ivan; Kranakis, Evangelos; Krizanc, Danny; Urrutia, Jorge: On the page number of RNA secondary structures with pseudoknots (2012)
  12. Clote, Peter; Ponty, Yann; Steyaert, Jean-Marc: Expected distance between terminal nucleotides of RNA secondary structures (2012)
  13. Seligmann, Hervé: Overlapping genes coded in the 3’-to-5’-direction in mitochondrial genes and 3’-to-5’ polymerization of non-complementary RNA by an `invertase’ (2012)
  14. Backofen, Rolf; Tsur, Dekel; Zakov, Shay; Ziv-Ukelson, Michal: Sparse RNA folding: time and space efficient algorithms (2011)
  15. Fang, Li Tai: The end-to-end distance of RNA as a randomly self-paired polymer (2011)
  16. Hower, Valerie; Heitsch, Christine E.: Parametric analysis of RNA branching configurations (2011)
  17. Mückstein, Ulrike; Leparc, Germán G.; Posekany, Alexandra; Hofacker, Ivo L.; Kreil, David P.: Hybridization thermodynamics of nimblegen microarrays (2010) ioport
  18. Seligmann, Hervé: The ambush hypothesis at the whole-organism level: off frame, `hidden’ stops in vertebrate mitochondrial genes increase developmental stability (2010)
  19. Arslan, Erdem; Laurenzi, Ian J.: An efficient algorithm for the stochastic simulation of the hybridization of DNA to microarrays (2009) ioport
  20. Backofen, Rolf; Tsur, Dekel; Zakov, Shay; Ziv-Ukelson, Michal: Sparse RNA folding: time and space efficient algorithms (2009)

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