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Related Experiment Videos

Projector: automatic contig mapping for gap closure purposes.

Sacha A F T van Hijum1, Aldert L Zomer, Oscar P Kuipers

  • 1Molecular Genetics, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, PO Box 14, 9750 AA Haren, The Netherlands. s.a.f.t.van.hijum@biol.rug.nl

Nucleic Acids Research
|November 7, 2003
PubMed
Summary

Projector software automatically positions genome contigs, improving assembly quality for prokaryotic genome projects. This efficient method aids in closing gaps during late-stage genome sequencing.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Genome sequencing projects generate numerous DNA contigs that require assembly.
  • Closing gaps in draft genomes is crucial for complete genome annotation and analysis.
  • Existing methods for contig positioning can be labor-intensive and time-consuming.

Purpose of the Study:

  • To develop and evaluate Projector, a novel software tool for automatic contig positioning.
  • To assess the efficiency of Projector in closing gaps in prokaryotic genomes.
  • To improve the quality of draft genome assemblies using Projector.

Main Methods:

  • Projector was used to map contigs from Lactococcus lactis MG1363 against the L. lactis IL1403 reference genome.
  • The software facilitated the identification of contig positions and aided in gap closure strategies.

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  • Polymerase chain reaction (PCR) was employed for gap closure validation.

    • Main Results:

    • Projector successfully mapped 84 contigs (81% of assembly nucleotides) of L. lactis MG1363.
    • Ninety-three percent of gap closure PCRs were successful, indicating high accuracy.
    • Significant improvements in N50 and N80 values were observed, signifying enhanced assembly quality.

    Conclusions:

    • Projector offers an efficient solution for automatic contig positioning in prokaryotic genome assembly.
    • The tool effectively aids in closing gaps, particularly in late-stage sequencing projects.
    • Projector enhances overall genome assembly quality, supporting ongoing bacterial genome research.