Nucleotide sequence alignment using sparse coding and belief propagation.

TitleNucleotide sequence alignment using sparse coding and belief propagation.
Publication TypeJournal Article
Year of Publication2013
AuthorsRoozgard, A, Barzigar, N, Wang, S, Jiang, X, Ohno-Machado, L, Cheng, S
JournalConf Proc IEEE Eng Med Biol Soc
Volume2013
Pagination588-91
Date Published2013 Jul
ISSN1557-170X
iDASH CategoryGenomics
AbstractAdvances in DNA information extraction techniques have led to huge sequenced genomes from organisms spanning the tree of life. This increasing amount of genomic information requires tools for comparison of the nucleotide sequences. In this paper, we propose a novel nucleotide sequence alignment method based on sparse coding and belief propagation to compare the similarity of the nucleotide sequences. We used the neighbors of each nucleotide as features, and then we employed sparse coding to find a set of candidate nucleotides. To select optimum matches, belief propagation was subsequently applied to these candidate nucleotides. Experimental results show that the proposed approach is able to robustly align nucleotide sequences and is competitive to SOAPaligner [1] and BWA [2].
DOI10.1109/EMBC.2013.6609568
Alternate JournalConf Proc IEEE Eng Med Biol Soc
PubMed ID24109755