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Nucleic Acids Research 2005 33(Web Server Issue):W573-W576; doi:10.1093/nar/gki424
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© The Author 2005. Published by Oxford University Press. All rights reserved
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Article

Stitchprofiles.uio.no: analysis of partly melted DNA conformations using stitch profiles

Eivind Tøstesen*, Geir Ivar Jerstad1 and Eivind Hovig

The Norwegian Radium Hospital N-0310 Oslo, Norway 1Department of Informatics, University of Oslo N–0316 Oslo, Norway

*To whom correspondence should be addressed. Tel: +47 22935392; Fax: +47 22522421; Email: eivind.tostesen{at}medisin.uio.no

Received February 14, 2005. Revised March 23, 2005. Accepted March 23, 2005.

In this study, we describe a web server that performs computations on DNA melting, thus predicting the localized separation of the two strands for sequences provided by the users. The output types are stitch profiles, melting curves, probability profiles, etc. Stitch profile diagrams visualize the ensemble of alternative conformations that DNA can adopt with different probabilities. For example, a stitch profile shows the possible loop openings in terms of their locations, sizes, probabilities and fluctuations at a given temperature. Sequences with lengths up to several tens or hundreds of kilobase pairs can be analysed. The tools are freely available at http://stitchprofiles.uio.no.


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