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Kohdista: an efficient method to index and query possible Rmap alignments.

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Algorithms for Molecular Biology : AMB
|December 24, 2019
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Summary

Kohdista efficiently aligns single molecule maps (Rmaps) by treating alignment as automaton path matching. This novel index-based algorithm successfully identifies high-quality Rmap alignments, even for large genomes.

Keywords:
FM-indexGraph algorithmsIndex based data structuresOptical mapping

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Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • Genome-wide optical maps provide high-resolution restriction site data.
  • Assembling these maps from raw data (Rmaps) is challenging due to high error rates.

Purpose of the Study:

  • To develop an efficient algorithm for aligning single molecule maps (Rmaps).

Main Methods:

  • Introduced Kohdista, an index-based algorithm for pairwise Rmap alignment.
  • Formulated alignment as automaton path matching using Generalized Compressed Suffix Array (GCSA) and wavelet trees.

Main Results:

  • Kohdista successfully finds alignments between simulated Rmaps from overlapping genomic regions.
  • Validated on simulated E. coli data.

Conclusions:

  • Kohdista is uniquely capable of finding numerous high-quality Rmap alignments for large eukaryotes in practical timeframes.