Improved alignment of homologous DNA sequences

Stojanov, Done and Martinovska, Cveta (2014) Improved alignment of homologous DNA sequences. Annals of West University of Timişoara, ser. Biology, 16 (2). pp. 97-106. ISSN 1453-7680


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A new aligning approach for homologous DNA sequences is presented, being faster than the standard dynamic programming based implementations. Searching for exact and non-crossing hits as fast as possible, tracking hits’ positions in a data vector,being dynamically sorted in ascending order, regarding the starting positions of the hits being identified, the time complexity of the methodology is O(knlog2m), such as: k is the number of exact, non-crossing hits, n is the length of the larger DNA sequence andm is the length of the shorter DNA sequence. The space complexity is linear O(k), what is favorable especially if larger DNA sequences have to be aligned, such as the inequality k < m is satisfied.

Item Type: Article
Subjects: Natural sciences > Computer and information sciences
Divisions: Faculty of Computer Science
Depositing User: Done Stojanov
Date Deposited: 16 Jan 2014 14:16
Last Modified: 21 Jan 2014 08:27

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