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WindowMasker: window-based masker for sequenced genomes.

Aleksandr Morgulis1, E Michael Gertz, Alejandro A Schäffer

  • 1National Center for Biotechnology Information, National Institutes of Health, Department of Health and Human Services Building 38A, Room 1003N, 8600 Rockville Pike, Bethesda, MD 20894, USA.

Bioinformatics (Oxford, England)
|November 17, 2005
PubMed
Summary
This summary is machine-generated.

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WindowMasker (WM) is a new, fast tool for masking repetitive DNA sequences in genomes. It improves DNA database search results by efficiently identifying and removing repetitive elements without needing external libraries.

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Repetitive DNA sequences complicate DNA database searches.
  • Existing tools like RepeatMasker/Maskeraid (RM) are slow and rely on curated libraries (e.g., RepBase) that may not cover newly sequenced genomes.

Purpose of the Study:

  • To develop a faster and more efficient software tool for identifying and masking repetitive DNA sequences in genomes.
  • To provide a method that does not require external repetitive sequence libraries.

Main Methods:

  • Developed WindowMasker (WM), a software tool that uses linear-time scans of genome sequence to identify repetitive DNA.
  • Compared BLAST search results on genomes masked by WM versus RM.

Main Results:

Related Experiment Videos

  • WM is orders of magnitude faster than RM.
  • WM masking yields more non-repetitive matches and fewer repetitive matches in DNA database searches, even for well-annotated genomes like the human genome.
  • WM performs effectively on draft genomes and transcribed regions.

Conclusions:

  • WindowMasker offers a significant speed improvement for repetitive DNA masking.
  • WM enhances the accuracy of DNA database searches by effectively masking repetitive elements.
  • WM is a valuable tool for genomic analysis, especially for novel or draft genomes.