Format

Send to

Choose Destination
Conf Proc IEEE Eng Med Biol Soc. 2013;2013:588-91. doi: 10.1109/EMBC.2013.6609568.

Nucleotide sequence alignment using sparse coding and belief propagation.

Abstract

Advances 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].

PMID:
24109755
PMCID:
PMC3909563
DOI:
10.1109/EMBC.2013.6609568
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for IEEE Engineering in Medicine and Biology Society Icon for PubMed Central
Loading ...
Support Center