Stitchprofiles.uio.no: analysis of partly melted DNA conformations using stitch profiles.
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.
Tøstesen
Eivind
E
The Norwegian Radium Hospital, N-0310 Oslo, Norway. eivind.tostesen@medisin.uio.no
Jerstad
Geir Ivar
GI
Hovig
Eivind
E
D000465:Algorithms; D004247:DNA / Q000737:chemistry*; D020407:Internet; D009691:Nucleic Acid Denaturation; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D013696:Temperature; D014584:User-Computer Interface
D004247:DNA