Search of Regions with Periodicity Using Random Position Weight Matrices in the Genome of C. elegans View Full Text


Ontology type: schema:Chapter     


Chapter Info

DATE

2017

AUTHORS

E. V. Korotkov , M. A. Korotkova

ABSTRACT

A mathematical method was developed in this study to determine tandem repeats in a DNA sequence. A multiple alignment of periods was calculated by direct optimization of the position-weight matrix (PWM) without using pairwise alignments or searching for similarity between periods. Random PWMs were used to develop a new mathematical algorithm for periodicity search. The developed algorithm was applied to analyze the DNA sequences of C. elegans genome. 25360 regions having a periodicity with length of 2 to 50 bases were found. On the average, a periodicity of ~4000 nucleotides was found to be associated with each region. A significant portion of the revealed regions have periods consisting of 10 and 11 nucleotides, multiple to 10 nucleotides and periods in the vicinity of 35 nucleotides. Only ~30% of the periods found were discovered early. This study discussed the origin of periodicity with insertions and deletions. More... »

PAGES

445-456

References to SciGraph publications

Book

TITLE

Bioinformatics and Biomedical Engineering

ISBN

978-3-319-56153-0
978-3-319-56154-7

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/978-3-319-56154-7_40

DOI

http://dx.doi.org/10.1007/978-3-319-56154-7_40

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1084744998


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