Stojanov, Done and Mileva, Aleksandra and Koceski, Saso (2012) A new, space-efficient local pairwise alignment methodology. Advanced Studies in Biology, 4 (2). pp. 85-93. ISSN 1313-9495
Full text not available from this repository.Abstract
Aligning large nucleotide sequences requires significant portion of the memory,
what in some cases is found as a limiting factor. Local pairwise alignment
methods require O(m) space, most of them being dynamic programming-based. In
this paper we present a new, space-efficient methodology and an algorithm for
optimal un-gapped local pairwise alignment, using non dynamic
programming-based approach.
A highest scoring un-gapped local alignment is found, identifying and
combining exact nucleotide matching regions, shifting one of the sequences over
the other. The number of shifts is score-dependent, what is a time complexity
advantage. An implementation of the proposed methodology was tested on
EMBL-EBI viroid genomes, always identifying an optimal un-gapped local
alignment, requiring on average m/2 space.
| Item Type: | Article |
|---|---|
| Subjects: | Natural sciences > Computer and information sciences |
| Divisions: | Faculty of Computer Science |
| Depositing User: | Aleksandra Mileva |
| Date Deposited: | 31 Oct 2012 09:02 |
| Last Modified: | 20 Dec 2012 11:28 |
| URI: | https://eprints.ugd.edu.mk/id/eprint/107 |
Actions (login required)
 |
View Item |