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

Eivind Tøstesen, Geir Ivar Jerstad, Eivind Hovig

Research output: Contribution to journalArticle

14 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
JournalNucleic acids research
Volume33
Issue numberSUPPL. 2
DOIs
StatePublished - Jul 1 2005

Fingerprint

Nucleic Acid Conformation
Nucleic Acid Denaturation
Freezing
Temperature

ASJC Scopus subject areas

  • Genetics

Cite this

Stitchprofiles.uio.no : Analysis of partly melted DNA conformations using stitch profiles. / Tøstesen, Eivind; Jerstad, Geir Ivar; Hovig, Eivind.

In: Nucleic acids research, Vol. 33, No. SUPPL. 2, 01.07.2005.

Research output: Contribution to journalArticle

@article{8a6dff02daf641089b962c24b02a8f25,
title = "Stitchprofiles.uio.no: Analysis of partly melted DNA conformations using stitch profiles",
abstract = "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.",
author = "Eivind T{\o}stesen and Jerstad, {Geir Ivar} and Eivind Hovig",
year = "2005",
month = "7",
day = "1",
doi = "10.1093/nar/gki424",
language = "English (US)",
volume = "33",
journal = "Nucleic Acids Research",
issn = "0305-1048",
publisher = "Oxford University Press",
number = "SUPPL. 2",

}

TY - JOUR

T1 - Stitchprofiles.uio.no

T2 - Analysis of partly melted DNA conformations using stitch profiles

AU - Tøstesen, Eivind

AU - Jerstad, Geir Ivar

AU - Hovig, Eivind

PY - 2005/7/1

Y1 - 2005/7/1

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=23144455034&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=23144455034&partnerID=8YFLogxK

U2 - 10.1093/nar/gki424

DO - 10.1093/nar/gki424

M3 - Article

C2 - 15980539

AN - SCOPUS:23144455034

VL - 33

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - SUPPL. 2

ER -