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CLONEPLACER: a software tool for simulating contig formation for ordered shotgun sequencing

G B Singh1, S A Krawetz

  • 1College of Engineering, Wayne State University, Detroit, Michigan 48202, USA.

Genomics
|January 20, 1995
PubMed
Summary
This summary is machine-generated.

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This software simulates large-scale mapping projects using ordered shotgun sequencing. It estimates map coverage, contig size, and gaps, aiding resource planning for megabase sequencing.

Area of Science:

  • Genomics and Bioinformatics
  • Computational Biology
  • Molecular Biology

Background:

  • Large-scale genome mapping projects require efficient strategies for resource allocation.
  • Ordered shotgun sequencing is a common approach for physical map construction.
  • Predictive tools are needed to estimate project parameters before initiation.

Purpose of the Study:

  • To introduce CLONEPLACER, a software tool for simulating large-scale regional mapping.
  • To provide a means for estimating resource requirements for megabase mapping and sequencing projects.
  • To guide the development of optimal strategies for complex genomic endeavors.

Main Methods:

  • Simulation of large-scale regional mapping using an ordered shotgun sequencing approach.

Related Experiment Videos

  • Analysis routines to estimate physical map coverage depth.
  • Calculation of the largest contig formed and the number of remaining gaps.

    • Main Results:

    • The software provides estimates of key mapping project parameters.
    • Detailed listings of contig spans within the physical map are generated.
    • An a priori method for estimating required resources is presented.

    Conclusions:

    • CLONEPLACER offers a valuable tool for planning and strategizing large-scale sequencing projects.
    • The software aids in optimizing resource allocation and predicting project outcomes.
    • It serves as a guide for deriving the most effective mapping strategies.