DINAMelt

DINAMelt web server for nucleic acid melting prediction. The DINAMelt web server simulates the melting of one or two single-stranded nucleic acids in solution. The goal is to predict not just a melting temperature for a hybridized pair of nucleic acids, but entire equilibrium melting profiles as a function of temperature. The two molecules are not required to be complementary, nor must the two strand concentrations be equal. Competition among different molecular species is automatically taken into account. Calculations consider not only the heterodimer, but also the two possible homodimers, as well as the folding of each single-stranded molecule. For each of these five molecular species, free energies are computed by summing Boltzmann factors over every possible hybridized or folded state. For temperatures within a user-specified range, calculations predict species mole fractions together with the free energy, enthalpy, entropy and heat capacity of the ensemble. Ultraviolet (UV) absorbance at 260 nm is simulated using published extinction coefficients and computed base pair probabilities. All results are available as text files and plots are provided for species concentrations, heat capacity and UV absorbance versus temperature. This server is connected to an active research program and should evolve as new theory and software are developed. The server URL is http://www.bioinfo.rpi.edu/applications/hybrid/.


References in zbMATH (referenced in 12 articles )

Showing results 1 to 12 of 12.
Sorted by year (citations)

  1. Komiya, Ken; Yamamura, Masayuki: Cascading DNA generation reaction for controlling DNA nanomachines at a physiological temperature (2015) ioport
  2. Seligmann, Hervé: Error compensation of tRNA misacylation by codon-anticodon mismatch prevents translational amino acid misinsertion (2011)
  3. Høvik, Hedda; Chen, Tsute: Dynamic probe selection for studying microbial transcriptome with high-density genomic tiling microarrays (2010) ioport
  4. Mückstein, Ulrike; Leparc, Germán G.; Posekany, Alexandra; Hofacker, Ivo L.; Kreil, David P.: Hybridization thermodynamics of nimblegen microarrays (2010) ioport
  5. Tulpan, Dan C.; Andronescu, Mirela; Leger, Serge: Free energy estimation of short DNA duplex hybridizations (2010) ioport
  6. Perez-Bello, Alcides; Munteanu, Cristian Robert; Ubeira, Florencio M.; Lopes De Magalhães, Alexandre; Uriarte, Eugenio; González-Díaz, Humberto: Alignment-free prediction of mycobacterial DNA promoters based on pseudo-folding lattice network or star-graph topological indices (2009)
  7. Clote, Peter: Introduction to special issue on RNA (2008)
  8. Ponty, Yann: Efficient sampling of RNA secondary structures from the Boltzmann ensemble of low-energy (2008)
  9. 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)
  10. Gąsieniec, Leszek; Li, Cindy Y.; Sant, Paul; Wong, Prudence W. H.: Randomized probe selection algorithm for microarray design (2007)
  11. Gharaibeh, Raad Z.; Fodor, Anthony A.; Gibas, Cynthia J.: Software note: using probe secondary structure information to enhance Affymetrix GeneChip background estimates (2007)
  12. Markham, Nicholas R.; Zuker, Michael: Dinamelt web server for nucleic acid melting prediction. (2005) ioport