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. 2003 Jul 1;31(13):3819-21.
doi: 10.1093/nar/gkg562.

WEB-THERMODYN: Sequence analysis software for profiling DNA helical stability

Yanlin Huang  1 , David Kowalski
Affiliations

WEB-THERMODYN: Sequence analysis software for profiling DNA helical stability

Yanlin Huang et al. Nucleic Acids Res. .

Abstract

WEB-THERMODYN analyzes DNA sequences and computes the DNA helical stability, i.e. the free energy required to unwind and separate the strands of the double helix. A helical stability profile across a selected DNA region or the entire sequence is generated by sliding-window analysis. WEB-THERMODYN can predict sites of low helical stability present at regulatory regions for transcription and replication and can be used to test the influence of mutations. The program can be accessed at: http://wings.buffalo.edu/gsa/dna/dk/WEBTHERMODYN/.

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Figures

Figure 1
Figure 1
WEB-THERMODYN output page (see text). Analysis of an S.cerevisiae chromosome III segment (positions 100001 to 110000) in a region containing a replication origin (ARS307) and two gene coding regions. Free energy minima at marks 1 and 2 occur at sequence positions that overlap the replication origin in the DUE region (6). Gene coding regions with elevated free energies flank the positions of the energy minima at the replication origin.
Figure 1
Figure 1
WEB-THERMODYN output page (see text). Analysis of an S.cerevisiae chromosome III segment (positions 100001 to 110000) in a region containing a replication origin (ARS307) and two gene coding regions. Free energy minima at marks 1 and 2 occur at sequence positions that overlap the replication origin in the DUE region (6). Gene coding regions with elevated free energies flank the positions of the energy minima at the replication origin.
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