Progressive alignment of genomic signals by multiple dynamic time warping
Language English Country England, Great Britain Media print-electronic
Document type Journal Article, Research Support, Non-U.S. Gov't
PubMed
26300069
DOI
10.1016/j.jtbi.2015.08.007
PII: S0022-5193(15)00395-1
Knihovny.cz E-resources
- Keywords
- Correlation, Genomic signal processing, Multiple alignment, Phylogenetic tree, Similarity distance,
- MeSH
- Algorithms MeSH
- RNA, Bacterial genetics MeSH
- Species Specificity MeSH
- Phylogeny MeSH
- Genome, Bacterial * MeSH
- Genomics methods MeSH
- Signal Processing, Computer-Assisted MeSH
- RNA, Ribosomal, 18S genetics MeSH
- Sequence Alignment methods MeSH
- Computational Biology methods MeSH
- Animals MeSH
- Check Tag
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Names of Substances
- RNA, Bacterial MeSH
- RNA, Ribosomal, 18S MeSH
This paper presents the utilization of progressive alignment principle for positional adjustment of a set of genomic signals with different lengths. The new method of multiple alignment of signals based on dynamic time warping is tested for the purpose of evaluating the similarity of different length genes in phylogenetic studies. Two sets of phylogenetic markers were used to demonstrate the effectiveness of the evaluation of intraspecies and interspecies genetic variability. The part of the proposed method is modification of pairwise alignment of two signals by dynamic time warping with using correlation in a sliding window. The correlation based dynamic time warping allows more accurate alignment dependent on local homologies in sequences without the need of scoring matrix or evolutionary models, because mutual similarities of residues are included in the numerical code of signals.
References provided by Crossref.org
Advanced DNA fingerprint genotyping based on a model developed from real chip electrophoresis data
A degeneration-reducing criterion for optimal digital mapping of genetic codes
