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zPicture: dynamic alignment and visualization tool for analyzing conservation profiles.

Ivan Ovcharenko1, Gabriela G Loots, Ross C Hardison

  • 1Energy, Environment, Biology and Institutional Computing, Lawrence Livermore National Laboratory, Livermore, California 94550, USA.

Genome Research
|March 3, 2004
PubMed
Summary
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zPicture is a web tool for identifying evolutionarily conserved regions (ECRs) in DNA sequences. It aids in discovering functional elements and transcription factor binding sites across diverse genomes.

Area of Science:

  • Genomics
  • Bioinformatics
  • Evolutionary Biology

Background:

  • Comparative sequence analysis is crucial for identifying conserved functional elements.
  • Evolutionarily conserved regions (ECRs) provide insights into biological function.
  • Identifying ECRs can be challenging, especially in conserved genomic backgrounds.

Purpose of the Study:

  • Introduce zPicture, an interactive web-based tool for sequence alignment and visualization.
  • Enable dynamic generation of conservation profiles and identification of ECRs.
  • Facilitate transcription factor binding-site analysis and integration with genome browsers.

Main Methods:

  • Interactive web-based sequence alignment and visualization.
  • Flexible parameter adjustment for differential ECR prediction.

Related Experiment Videos

  • Integration with rVista for transcription factor binding-site analysis.
  • Linking to UCSC Genome Browser for sequence and annotation extraction.

    • Main Results:

    • Demonstrated identification of a known regulatory element in the HOXD locus.
    • Successfully pinpointed two ECRs with specific transcription factor binding sites in the HBB complex.
    • Showcased applicability to non-vertebrate and microbial genomes.

    Conclusions:

    • zPicture offers a flexible and interactive approach to ECR identification.
    • The tool aids in discovering functional genomic elements and regulatory sites.
    • zPicture enhances comparative genomics analysis across a wide range of organisms.