Novel graphical representation of genome sequence and its applications in similarity analysis
AbstractIn order to compare different genome sequences, an alignment-free method has been proposed. Considering the essential property of sequence is sequentiality, we define a compound transformation which transforms a genome sequence into a sparse 16 by L−1 matrix M based on 16 kinds of 2-mer (dinucleotides). Furthermore, we found the transformation above-mentioned is an order-preserving transformation (OPT). Based on the theory of matrix analysis, we derive a 16-dimensional vector to characterize a genome sequence via singular value decomposition (SVD) of M. Finally, we analyze the similarities among multiple sequences from 20 eutherian species. The experiment results show that our approach performs well in the field of sequence analysis.
Download InfoIf you experience problems downloading a file, check if you have the proper application to view it first. In case of further problems read the IDEAS help page. Note that these files are not on the IDEAS site. Please be patient as the files may be large.
Bibliographic InfoArticle provided by Elsevier in its journal Physica A: Statistical Mechanics and its Applications.
Volume (Year): 391 (2012)
Issue (Month): 23 ()
Contact details of provider:
Web page: http://www.journals.elsevier.com/physica-a-statistical-mechpplications/
Genome sequence; Order-preserving; Singular value decomposition (SVD); Similarity analysis;
You can help add them by filling out this form.
reading list or among the top items on IDEAS.Access and download statisticsgeneral information about how to correct material in RePEc.
If references are entirely missing, you can add them using this form.