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Related Experiment Videos

A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis

E L Sonnhammer1, R Durbin

  • 1Sanger Centre, Hinxton Hall, Cambridge, UK.

Gene
|December 29, 1995
PubMed
Summary
This summary is machine-generated.

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DOTTER2 is a novel dot-plot program for comparing DNA and protein sequences. Its interactive

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Dot-matrix plots offer detailed sequence comparisons.
  • Existing tools may require recalculation for varying stringency.
  • Efficient sequence analysis is crucial for genomic studies.

Purpose of the Study:

  • Introduce DOTTER2, a new dot-plot program for sequence comparison.
  • Highlight DOTTER2's interactive stringency adjustment feature.
  • Demonstrate DOTTER2's utility in gene modeling and sequence analysis.

Main Methods:

  • Developed DOTTER2, a dot-plot program for X-windows.
  • Implemented a 'Greyramp tool' for interactive stringency cutoff adjustment.
  • Integrated DOTTER2 with ACEDB3 genomic database and BLIXEM homology viewer.

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Main Results:

  • DOTTER2 allows interactive exploration of sequence similarity at varying stringencies without recalculation.
  • The program efficiently handles long sequences (e.g., cosmids) due to linear space complexity.
  • Integration with ACEDB3 and BLIXEM facilitates rapid identification of sequence matches and aids gene modeling.

Conclusions:

  • DOTTER2 provides a powerful and flexible tool for detailed DNA and protein sequence comparison.
  • The interactive Greyramp tool enhances visualization and analysis of sequence data.
  • DOTTER2's integration and efficiency improve genomic analysis workflows, particularly in gene modeling.