Literature DB >> 12824427

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

Yanlin Huang1, David Kowalski.   

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/.

Entities:  

Mesh：

Substances：

Year:  2003        PMID： 12824427      PMCID： PMC168969          DOI： 10.1093/nar/gkg562

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN： 0305-1048            Impact factor:   16.971


  19 in total

1.  Biological significance of unwinding capability of nuclear matrix-associating DNAs.

Authors:  J Bode; Y Kohwi; L Dickinson; T Joh; D Klehr; C Mielke; T Kohwi-Shigematsu
Journal:  Science       Date:  1992-01-10       Impact factor: 47.728

2.  Predicting DNA duplex stability from the base sequence.

Authors:  K J Breslauer; R Frank; H Blöcker; L A Marky
Journal:  Proc Natl Acad Sci U S A       Date:  1986-06       Impact factor: 11.205

3.  Duplex opening by dnaA protein at novel sequences in initiation of replication at the origin of the E. coli chromosome.

Authors:  D Bramhill; A Kornberg
Journal:  Cell       Date:  1988-03-11       Impact factor: 41.582

4.  Torsional stress stabilizes extended base unpairing in suppressor sites flanking immunoglobulin heavy chain enhancer.

Authors:  T Kohwi-Shigematsu; Y Kohwi
Journal:  Biochemistry       Date:  1990-10-16       Impact factor: 3.162

5.  Stable DNA unwinding, not "breathing," accounts for single-strand-specific nuclease hypersensitivity of specific A+T-rich sequences.

Authors:  D Kowalski; D A Natale; M J Eddy
Journal:  Proc Natl Acad Sci U S A       Date:  1988-12       Impact factor: 11.205

6.  The inefficient replication origin from yeast ribosomal DNA is naturally impaired in the ARS consensus sequence and in DNA unwinding.

Authors:  C A Miller; R M Umek; D Kowalski
Journal:  Nucleic Acids Res       Date:  1999-10-01       Impact factor: 16.971

7.  Identification of a candidate regulatory region in the human CD8 gene complex by colocalization of DNase I hypersensitive sites and matrix attachment regions which bind SATB1 and GATA-3.

Authors:  Lynda J Kieffer; John M Greally; Inna Landres; Shanta Nag; Yuko Nakajima; Terumi Kohwi-Shigematsu; Paula B Kavathas
Journal:  J Immunol       Date:  2002-04-15       Impact factor: 5.422

8.  The ease of DNA unwinding as a determinant of initiation at yeast replication origins.

Authors:  R M Umek; D Kowalski
Journal:  Cell       Date:  1988-02-26       Impact factor: 41.582

9.  Localized melting and structural changes in the SV40 origin of replication induced by T-antigen.

Authors:  J A Borowiec; J Hurwitz
Journal:  EMBO J       Date:  1988-10       Impact factor: 11.598

10.  The DNA unwinding element: a novel, cis-acting component that facilitates opening of the Escherichia coli replication origin.

Authors:  D Kowalski; M J Eddy
Journal:  EMBO J       Date:  1989-12-20       Impact factor: 11.598
View more
  25 in total

1.  DNA-energetics-based analyses suggest additional genes in prokaryotes.

Authors:  Garima Khandelwal; Jalaj Gupta; B Jayaram
Journal:  J Biosci       Date:  2012-07       Impact factor: 1.826

2.  Chromosomal context and replication properties of ARS plasmids in Schizosaccharomyces pombe.

Authors:  Aditya S Pratihar; Vishnu P Tripathi; Mukesh P Yadav; Dharani D Dubey
Journal:  J Biosci       Date:  2015-12       Impact factor: 1.826

3.  Recruitment of ORC or CDC6 to DNA is sufficient to create an artificial origin of replication in mammalian cells.

Authors:  David Y Takeda; Yoshiyuki Shibata; Jeffrey D Parvin; Anindya Dutta
Journal:  Genes Dev       Date:  2005-12-01       Impact factor: 11.361

4.  A statistical thermodynamic model for investigating the stability of DNA sequences from oligonucleotides to genomes.

Authors:  Garima Khandelwal; Rebecca A Lee; B Jayaram; David L Beveridge
Journal:  Biophys J       Date:  2014-06-03       Impact factor: 4.033

5.  The Rep20 replication initiator from the pAG20 plasmid of Acetobacter aceti.

Authors:  Martin Babič; Zuzana Rešková; Juraj Bugala; Viera Cimová; Peter Grones; Jozef Grones
Journal:  Mol Biotechnol       Date:  2014-01       Impact factor: 2.695

6.  Plant-derived transfer DNAs.

Authors:  Caius M Rommens; Oleg Bougri; Hua Yan; Jaime M Humara; Joanna Owen; Kathy Swords; Jingsong Ye
Journal:  Plant Physiol       Date:  2005-10-21       Impact factor: 8.340

7.  TPV1, the first virus isolated from the hyperthermophilic genus Thermococcus.

Authors:  Aurore Gorlas; Eugene V Koonin; Nadège Bienvenu; Daniel Prieur; Claire Geslin
Journal:  Environ Microbiol       Date:  2011-12-12       Impact factor: 5.491

8.  Nucleotide sequence, structural organization and length heterogeneity of ribosomal DNA intergenic spacer in Quercus petraea (Matt.) Liebl. and Q. robur L.

Authors:  Natasa Bauer; Tomislav Horvat; Ivan Birus; Vedrana Vicić; Vlatka Zoldos
Journal:  Mol Genet Genomics       Date:  2008-12-04       Impact factor: 3.291

9.  Analysis of the first genome of a hyperthermophilic marine virus-like particle, PAV1, isolated from Pyrococcus abyssi.

Authors:  C Geslin; M Gaillard; D Flament; K Rouault; M Le Romancer; D Prieur; G Erauso
Journal:  J Bacteriol       Date:  2007-04-20       Impact factor: 3.490

10.  Genetic and epigenetic determinants mediate proneness of oncogene breakpoint sites for involvement in TCR translocations.

Authors:  N S D Larmonie; A van der Spek; A J J C Bogers; J J M van Dongen; A W Langerak
Journal:  Genes Immun       Date:  2013-12-05       Impact factor: 2.676
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.