DNA Melting - About


Welcome to stitchprofiles.uio.no

This server performs web-based computations on DNA melting, thus predicting the localized separation of the two strands for sequences provided by the users.

The primary tool here is the stitch profile - a diagram representing the alternative conformations that partly melted DNA can adopt. This new type of diagram is an alternative to the ordinary probability profiles for describing the conformations and their statistics at a given temperature.

In addition to stitch profile diagrams, the server can also plot the usual melting profiles such as melting curves, probability profiles, and temperature profiles.


This website is supported by
This website was developed and maintained by: NCBI
We used this service from NCBI to get the sequences: EFetch

Citation instructions and conditions of use

The web tools require no registration and are freely available to both academic and commercial users. The source code is, however, not available for downloading.

Please cite the following article when using output of computations on this server:

E. Tøstesen, G. I. Jerstad and E. Hovig (2005): Stitchprofiles.uio.no: Analysis of partly melted DNA conformations using stitch profiles. Nucl. Acids Res., 33, w573-w576. Doi:10.1093/nar/gki424.

The articles describing the algorithms running on this server can also be cited as appropriate: The DNA melting algorithm by Tøstesen et al. (2003) and the stitch profile algorithm by Tøstesen (2008).

Other material on this website is copyrighted.


Please email us with requests, problems, bugs and comments.


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E. Tøstesen (2008): A stitch in time: Efficient computation of genomic DNA melting bubbles. Algorithms for Molecular Biology, 3, 10. Doi:10.1186/1748-7188-3-10 (open access).

F. Liu, E. Tøstesen, J. K. Sundet, T.-K. Jenssen, C. Bock, G. I. Jerstad, W. G. Thilly and E. Hovig (2007): The human genomic melting map. PLoS Computational Biology, 3(5), e93. Doi:10.1371/journal.pcbi.0030093. Project website: Meltmap.uio.no.

G. I. Jerstad, E. Tøstesen, Torbjørn Rognes and E. Hovig (2006): Genome-wide Comparison of DNA Melting Bubbles and Ensembl's Genomic Annotations. Poster at ISMB 2006 in Fortaleza, Brazil, August 6-10. Poster pdf (784KB) here..

G. I. Jerstad (2006): Merging the physical properties of DNA with genomic annotations in Ensembl. Master thesis, University of Oslo. Fulltext here.

E. Tøstesen, G. I. Jerstad and E. Hovig (2005): Stitchprofiles.uio.no: Analysis of partly melted DNA conformations using stitch profiles. Nucl. Acids Res., 33 (web server issue), w573-w576. Doi:10.1093/nar/gki424 (open access).

E. Tøstesen (2005): Partly melted DNA conformations obtained with a probability peak finding method. Phys. Rev. E, 71, 061922. Doi:10.1103/PhysRevE.71.061922 (with supplementary material). Preprint at arxiv.org: q-bio.BM/0404019.

E. Tøstesen, F. Liu, T.-K. Jenssen and E. Hovig (2003): Speed-up of DNA melting algorithm with complete nearest neighbor properties. Biopolymers, 70, 364-376. Doi:10.1002/bip.10495. Preprint at arxiv.org: q-bio.BM/0401011.

R. D. Blake and S. G. Delcourt (1998): Thermal stability of DNA. Nucl. Acids Res., 26, 3323-3332.

R. Blossey and E. Carlon (2003): Reparametrizing loop entropy weights: Effect on DNA melting curves. Phys. Rev. E, 68, 061911. Preprint at arxiv.org: cond-mat/0212457.

J. SantaLucia, Jr. (1998): A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc Natl Acad Sci, 95, 1460-1465

O. Gotoh and Y. Tagashira (1981): Stabilities of nearest-neighbor doublets in double-helical DNA determined by fitting calculated melting profiles to observed profiles. Biopolymers, 20, 1033-1042.

M. Fixman and J. J. Freire (1977): Theory of DNA melting curves. Biopolymers, 16, 2693-2704.

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