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A local alignment tool for very long DNA sequences

K M Chao1, J Zhang, J Ostell

  • 1Department of Computer Science and Engineering, Pennsylvania State University, University Park 16802, USA.

Computer Applications in the Biosciences : CABIOS
|April 1, 1995
PubMed
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This study introduces sim2, a program for aligning long DNA sequences efficiently. It aids in analyzing sequence differences and resolving inconsistencies for applications like contig-building.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Accurate alignment of long DNA sequences is crucial for genomic research.
  • Existing tools may face limitations with sequences hundreds of kilobases long.

Purpose of the Study:

  • To present sim2, a practical program for local alignment of large DNA sequences.
  • To demonstrate sim2's utility in contig-building and analyzing sequence variations.

Main Methods:

  • sim2 constructs n best non-intersecting chains of fragments (e.g., identical 5-tuples).
  • Chains are refined to provide optimal local alignments.
  • The program is designed for efficient space usage and cross-platform compatibility.

Main Results:

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  • sim2 successfully aligns DNA sequences up to hundreds of kilobases.
  • The program demonstrates efficient performance and broad platform support.
  • Application to Escherichia coli DNA sequences showcases its utility.

Conclusions:

  • sim2 offers a practical and efficient solution for aligning long DNA sequences.
  • The tool facilitates contig-building, enabling better analysis of sequence differences and inconsistencies.
  • sim2 integrates with visualization tools like ChromoScope for enhanced usability.