Nucleotide sequence alignment using sparse coding and belief propagation
Year: 2013
Type: conference-paper
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].
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
Awards: iDASH: Integrating Data for Analysis, Anonymization, and Sharing, San Diego Clinical and Translational Research Institute, Protection of Records: Privacy (PReP) Technology for Medical Research, SCANNER: SCALABLE NATIONAL NETWORK FOR EFFECTIVENESS RESEARCH, G6447849018, Phenotype Discovery in NHLBI Genomic Studies (PhD)
OpenAlex ID: W2004356294