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Related Experiment Videos

CONTIG EXPLORER: interactive marker-content map assembly

P M Nadkarni1, A Banks, K Montgomery

  • 1Center for Medical Informatics, Yale School of Medicine, New Haven, Connecticut 06520, USA. nadkarni@cs.yale.edu

Genomics
|February 1, 1996
PubMed
Summary

CONTIG EXPLORER software aids in assembling STS-content maps by enabling interactive analysis and evaluation of marker orders. This tool helps researchers reliably place markers on physical maps and design experiments to reduce ambiguity in STS ordering.

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Area of Science:

  • Genomics and Bioinformatics
  • Computational Biology
  • Physical Mapping

Background:

  • STS-content mapping involves determining the order of markers on a chromosome, but multiple optimal orders can exist.
  • Reliably placing markers on a physical map requires tools for sensitivity analysis and interactive reassembly of data subsets.
  • Evaluating arbitrary marker orders is crucial for refining physical maps and experimental design.

Purpose of the Study:

  • To introduce CONTIG EXPLORER, a software package for interactive assembly of STS-content maps.
  • To facilitate exploratory sensitivity analysis and interactive reassembly of mapping data.
  • To assist in evaluating user-specified marker orders and reducing ambiguity in STS ordering.

Main Methods:

  • Development of CONTIG EXPLORER software for interactive STS-content map assembly.

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  • Implementation of features for exploratory sensitivity analysis and interactive reassembly with varying data subsets.
  • Comparison of CONTIG EXPLORER with SEGMAP and CONTIGMAKER using a specific region of chromosome 12p.

    • Main Results:

    • CONTIG EXPLORER provides interactive tools for analyzing STS-content map assembly.
    • The software facilitates the evaluation of marker order reliability and experimental design.
    • Comparative analysis demonstrated the utility of CONTIG EXPLORER against existing assembly programs.

    Conclusions:

    • CONTIG EXPLORER enhances the process of physical map construction by enabling detailed analysis of marker order.
    • The interactive features of CONTIG EXPLORER aid researchers in resolving ambiguities in STS mapping.
    • This software assists in designing more effective laboratory experiments for accurate chromosome mapping.