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

Kristian Vlahovicek1, László Kaján, Sándor Pongor

  • 1Protein Structure and Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, Area Science Park, 34012 Trieste, Italy.

Nucleic Acids Research
|June 26, 2003
PubMed
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This summary is machine-generated.

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This study introduces a suite of bioinformatics servers for DNA sequence analysis, including tools for plotting physicochemical parameters, calculating DNA curvature, and modeling 3D DNA structures. An additional server enables statistical evaluation of introns across taxonomic groups.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Biology

Background:

  • Analyzing DNA sequences requires specialized tools for understanding structure and function.
  • Physicochemical properties, DNA curvature, and intron characteristics are crucial for molecular biology research.

Purpose of the Study:

  • To present a collection of web servers for comprehensive DNA sequence analysis.
  • To provide tools for visualizing DNA parameters, modeling structures, and evaluating introns.

Main Methods:

  • Web servers offering analysis of user-submitted DNA sequences.
  • Tools for plotting physicochemical and statistical parameters (plot.it).
  • DNA curvature calculation (bend.it) and 3D structure modeling (model.it).
  • Statistical evaluation of introns and splice sites (introns server).

Related Experiment Videos

Main Results:

  • Servers provide 1D and 2D plots for identifying specific DNA segments.
  • 3D DNA models are generated in PDB format for visualization.
  • Statistical analysis of intron length, base composition, and type is available.
  • Splice site analysis and exon-shuffling probability tests are included.

Conclusions:

  • The presented bioinformatics servers offer a versatile platform for diverse DNA sequence analyses.
  • These tools facilitate the localization of peculiar DNA segments, structural modeling, and evolutionary studies of introns.