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Literature DB >> 12824394

DNA analysis servers: plot.it, bend.it, model.it and IS.

Kristian Vlahovicek¹, László Kaján, Sándor Pongor.

Abstract

The WWW servers at http://www.icgeb.trieste.it/dna/ are dedicated to the analysis of user-submitted DNA sequences; plot.it creates parametric plots of 45 physicochemical, as well as statistical, parameters; bend.it calculates DNA curvature according to various methods. Both programs provide 1D as well as 2D plots that allow localisation of peculiar segments within the query. The server model.it creates 3D models of canonical or bent DNA starting from sequence data and presents the results in the form of a standard PDB file, directly viewable on the user's PC using any molecule manipulation program. The recently established introns server allows statistical evaluation of introns in various taxonomic groups and the comparison of taxonomic groups in terms of length, base composition, intron type etc. The options include the analysis of splice sites and a probability test for exon-shuffling.

Mesh：

Substances：
DNA

Year: 2003 PMID： 12824394 PMCID： PMC168966 DOI： 10.1093/nar/gkg559

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

12 in total

1. Model.it: building three dimensional DNA models from sequence data.

Authors: K Vlahovicek; S Pongor
Journal: Bioinformatics Date: 2000-11 Impact factor: 6.937

2. IS: a web-site for intron statistics.

Authors: Endre Barta; László Kaján; Sándor Pongor
Journal: Bioinformatics Date: 2003-03-01 Impact factor: 6.937

3. Curved DNA without A-A: experimental estimation of all 16 DNA wedge angles.

Authors: A Bolshoy; P McNamara; R E Harrington; E N Trifonov
Journal: Proc Natl Acad Sci U S A Date: 1991-03-15 Impact factor: 11.205

Review 4. Rod models of DNA: sequence-dependent anisotropic elastic modelling of local bending phenomena.

Authors: M G Munteanu; K Vlahovicek; S Parthasarathy; I Simon; S Pongor
Journal: Trends Biochem Sci Date: 1998-09 Impact factor: 13.807

Review 5. Evolution of the intron-exon structure of eukaryotic genes.

Authors: M Long; S J de Souza; W Gilbert
Journal: Curr Opin Genet Dev Date: 1995-12 Impact factor: 5.578

6. Correlation of intrinsic DNA curvature with DNA property periodicity.

Authors: A Gabrielian; S Pongor
Journal: FEBS Lett Date: 1996-09-09 Impact factor: 4.124

7. Statistical analysis of DNA duplex structural features.

Authors: N B Ulyanov; T L James
Journal: Methods Enzymol Date: 1995 Impact factor: 1.600

8. Influence of fluctuations on DNA curvature. A comparison of flexible and static wedge models of intrinsically bent DNA.

Authors: W K Olson; N L Marky; R L Jernigan; V B Zhurkin
Journal: J Mol Biol Date: 1993-07-20 Impact factor: 5.469

9. Statistical analysis of the exon-intron structure of higher and lower eukaryote genes.

Authors: E V Kriventseva; M S Gelfand
Journal: J Biomol Struct Dyn Date: 1999-10

Review 10. Trinucleotide models for DNA bending propensity: comparison of models based on DNaseI digestion and nucleosome packaging data.

Authors: I Brukner; R Sánchez; D Suck; S Pongor
Journal: J Biomol Struct Dyn Date: 1995-10

74 in total

1. Molecular characterization of UpaB and UpaC, two new autotransporter proteins of uropathogenic Escherichia coli CFT073.

Authors: Luke P Allsopp; Christophe Beloin; Glen C Ulett; Jaione Valle; Makrina Totsika; Orla Sherlock; Jean-Marc Ghigo; Mark A Schembri
Journal: Infect Immun Date: 2011-09-19 Impact factor: 3.441

2. Solution structure and DNA binding of the effector domain from the global regulator PrrA (RegA) from Rhodobacter sphaeroides: insights into DNA binding specificity.

Authors: Cédric Laguri; Mary K Phillips-Jones; Michael P Williamson
Journal: Nucleic Acids Res Date: 2003-12-01 Impact factor: 16.971

3. H-NS silences gfp, the green fluorescent protein gene: gfpTCD is a genetically Remastered gfp gene with reduced susceptibility to H-NS-mediated transcription silencing and with enhanced translation.

Authors: Colin P Corcoran; Andrew D S Cameron; Charles J Dorman
Journal: J Bacteriol Date: 2010-07-16 Impact factor: 3.490

DNA analysis servers: plot.it, bend.it, model.it and IS.

1. Model.it: building three dimensional DNA models from sequence data.

2. IS: a web-site for intron statistics.

3. Curved DNA without A-A: experimental estimation of all 16 DNA wedge angles.

Review 4. Rod models of DNA: sequence-dependent anisotropic elastic modelling of local bending phenomena.

Review 5. Evolution of the intron-exon structure of eukaryotic genes.

6. Correlation of intrinsic DNA curvature with DNA property periodicity.

7. Statistical analysis of DNA duplex structural features.

8. Influence of fluctuations on DNA curvature. A comparison of flexible and static wedge models of intrinsically bent DNA.

9. Statistical analysis of the exon-intron structure of higher and lower eukaryote genes.

Review 10. Trinucleotide models for DNA bending propensity: comparison of models based on DNaseI digestion and nucleosome packaging data.

1. Molecular characterization of UpaB and UpaC, two new autotransporter proteins of uropathogenic Escherichia coli CFT073.

2. Solution structure and DNA binding of the effector domain from the global regulator PrrA (RegA) from Rhodobacter sphaeroides: insights into DNA binding specificity.

3. H-NS silences gfp, the green fluorescent protein gene: gfpTCD is a genetically Remastered gfp gene with reduced susceptibility to H-NS-mediated transcription silencing and with enhanced translation.

4. Molecular characterization of the EhaG and UpaG trimeric autotransporter proteins from pathogenic Escherichia coli.

5. In vitro and in vivo analysis of the role of PrrA in Rhodobacter sphaeroides 2.4.1 hemA gene expression.

6. Probing a label-free local bend in DNA by single molecule tethered particle motion.

7. Agrobacterium tumefaciens C58 uses ActR and FnrN to control nirK and nor expression.

8. Intrinsic curvature associated with the coordinately regulated anthrax toxin gene promoters.

9. Characterization of the satellitome in lower vascular plants: the case of the endangered fern Vandenboschia speciosa.

10. Characterization of BNT2, an intrinsically curved DNA of Escherichia coli O157:H7.