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ShiftDetector: detection of shift mutations.

Eyal Seroussi1, Micha Ron, Darek Kedra

  • 1Institute of Animal Science, Volcani Center, Bet-Dagan 50250, Israel. seroussi@agri.huji.ac.il

Bioinformatics (Oxford, England)
|August 15, 2002
PubMed
Summary
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ShiftDetector identifies superimposed sequencing data caused by insertion/deletion mutations. This tool aids in base calling by analyzing trace files and reconstructing original DNA sequences.

Area of Science:

  • * Molecular Biology
  • * Bioinformatics

Background:

  • * Bi-allelic PCR products with insertion/deletion mutations create superimposed sequencing trace files.
  • * Existing base calling programs struggle with superimposed trace files, hindering analysis.

Purpose of the Study:

  • * To develop a computational tool, ShiftDetector, for analyzing superimposed sequencing trace files.
  • * To identify shift mutations (1-25 bases) within superimposed sequences.
  • * To reconstruct the original DNA sequences from superimposed data.

Main Methods:

  • * ShiftDetector analyzes sequencing trace files for superimposed sequences.
  • * It calculates a probability score indicating the presence of a shift mutation.
  • * The program reconstructs the sequences of the original molecules.

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Main Results:

  • * ShiftDetector successfully identifies superimposed trace files caused by shift mutations.
  • * The program provides a probability score for the shift mutation's existence.
  • * ShiftDetector reconstructs the original DNA sequences accurately.

Conclusions:

  • * ShiftDetector is a valuable tool for analyzing complex sequencing data.
  • * It overcomes limitations of current base calling programs for sequences with shift mutations.
  • * The software facilitates accurate DNA sequence reconstruction.