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The ITS2 Database
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A novel linear indexing method for strings under all internal nodes in a suffix tree.

Anas Al-Okaily1, Abdelghani Tbakhi2

  • 1Department of Cell Therapy and Applied Genomics, King Hussein Cancer Center, Amman, Jordan.

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|September 22, 2025
PubMed
Summary

This study introduces two linear-time algorithms for indexing suffix trees, enabling efficient tracking of string similarities and redundancies. These novel indexing methods enhance applications in DNA analysis and approximate pattern matching.

Keywords:
approximate pattern matchingmotif searchreads alignmentstrings indexingsuffix trees

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Area of Science:

  • Stringology
  • Data Structures
  • Bioinformatics

Background:

  • Suffix trees are essential in string processing.
  • Current methods lack efficient tracking of similarities across nodes.

Purpose of the Study:

  • To develop linear-time algorithms for indexing suffix trees.
  • To enable tracking of similarities and redundancies across internal nodes.

Main Methods:

  • Proposed a novel tree structure derived from suffix trees.
  • Introduced new indexing concepts for internal nodes.

Main Results:

  • Developed two linear-time algorithms for suffix tree indexing.
  • The new structure preserves the ability to track similarities and redundancies.

Conclusions:

  • The proposed indexing methods provide practical solutions.
  • Applications include DNA sequence analysis and approximate pattern matching.