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Proceedings Article

Algorithm to search for genomic rearrangements

[+] Author Affiliations
Katarzyna Nałęcz-Charkiewicz, Robert Nowak

Warsaw Univ. of Technology (Poland)

Proc. SPIE 8903, Photonics Applications in Astronomy, Communications, Industry, and High-Energy Physics Experiments 2013, 890319 (October 25, 2013); doi:10.1117/12.2032639
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From Conference Volume 8903

  • Photonics Applications in Astronomy, Communications, Industry, and High-Energy Physics Experiments 2013
  • Ryszard S. Romaniuk
  • Wilga, Poland | May 27, 2013

abstract

The aim of this article is to discuss the issue of comparing nucleotide sequences in order to detect chromosomal rearrangements (for example, in the study of genomes of two cucumber varieties, Polish and Chinese). Two basic algorithms for detecting rearrangements has been described: Smith-Waterman algorithm, as well as a new method of searching genetic markers in combination with Knuth-Morris-Pratt algorithm. The computer program in client-server architecture was developed. The algorithms properties were examined on genomes Escherichia coli and Arabidopsis thaliana genomes, and are prepared to compare two cucumber varieties, Polish and Chinese. The results are promising and further works are planned. © (2013) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only.

Topics

Algorithms ; Software
Citation

Katarzyna Nałęcz-Charkiewicz and Robert Nowak
" Algorithm to search for genomic rearrangements ", Proc. SPIE 8903, Photonics Applications in Astronomy, Communications, Industry, and High-Energy Physics Experiments 2013, 890319 (October 25, 2013); doi:10.1117/12.2032639; http://dx.doi.org/10.1117/12.2032639


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