Algorithm to search for genomic rearrangements

Katarzyna Nałęcz-Charkiewicz; Robert Nowak

doi:10.1117/12.2032639

25 October 2013 Algorithm to search for genomic rearrangements

Katarzyna Nałęcz-Charkiewicz, Robert Nowak

Proceedings Volume 8903, Photonics Applications in Astronomy, Communications, Industry, and High-Energy Physics Experiments 2013; 890319 (2013) https://doi.org/10.1117/12.2032639
Event: Photonics Applications in Astronomy, Communications, Industry, and High-Energy Physics Experiments 2013, 2013, Wilga, Poland

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.

Citation Download 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 (25 October 2013); https://doi.org/10.1117/12.2032639

ACCESS THE FULL ARTICLE

INSTITUTIONAL
Select your institution to access the SPIE Digital Library.

SELECT YOUR INSTITUTION

PERSONAL
Sign in with your SPIE account to access your personal subscriptions or to use specific features such as save to my library, sign up for alerts, save searches, etc.

PERSONAL SIGN IN

No SPIE Account? Create one

PURCHASE THIS CONTENT

SUBSCRIBE TO DIGITAL LIBRARY

50 downloads per 1-year subscription

Members: $195

Non-members: $335 ADD TO CART

25 downloads per 1 - year subscription

Members: $145

Non-members: $250 ADD TO CART

PURCHASE SINGLE ARTICLE

Includes PDF, HTML & Video, when available