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Related Experiment Video

Updated: May 18, 2026

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles
10:23

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Published on: July 11, 2025

Pattern matching in indeterminate and Arc-annotated sequences.

Md Tanvir Islam Aumi1, Tanaeem M Moosa, M Sohel Rahman

  • 1A l EDA Group, Department of CSE, BUET, Dhaka-1000, Bangladesh. tanviraumi@gmail.com

Recent Patents on DNA & Gene Sequences
|September 15, 2012
PubMed
Summary
This summary is machine-generated.

We developed fast algorithms for finding patterns in biological sequences, significantly improving the speed of analyzing genetic data and scanning for ncRNAs (non-coding RNAs) in human chromosomes.

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Last Updated: May 18, 2026

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07:49

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Biological sequences are often modeled using indeterminate Arc-Annotated sequences.
  • Efficient pattern matching is crucial for analyzing large biological datasets like reference genomes.

Purpose of the Study:

  • To present efficient algorithms for finding indeterminate Arc-Annotated patterns in references.
  • To apply these algorithms to scan for ncRNAs (non-coding RNAs) without pseudoknots.

Main Methods:

  • Developed algorithms with a time complexity of O(m + (nm)w), where n and m are string lengths and w is machine word size.
  • Assumed constant alphabet size, suitable for biological sequence modeling.

Main Results:

  • Algorithms achieve linear time for short patterns, enabling practical applications in genome analysis.
  • Successfully scanned three human chromosomes for ncRNA families in 2.5-4 minutes per chromosome.

Conclusions:

  • The presented algorithms offer significant efficiency gains for pattern matching in biological sequences.
  • The method demonstrates practical utility in rapidly scanning large genomic regions for specific RNA families.