Vector representations and related matrices of DNA primary sequence based on L-tuple.
We consider to construct 4(L)-components vectors for a DNA primary sequence based on the L-tuple. For two DNA sequences, using the corresponding vectors, we construct a set of L x L matrices called related matrix. The mathematical characterization from the constructed matrices have been selected to characterize the degree of similarity between the two DNA sequences. The search for similar sequences of a query sequence from a database of 39 library sequences and the construction of phylogenetic tree of H5N1 avian influenza virus illustrate the utility of the matrices for DNA sequences.
Liu
Ying-zhao
YZ
Department of Mathematics, Luoyang Normal University, Luoyang 471022, PR China. liuyingzhaoyz@yahoo.com.cn
Wang
Tian-ming
TM
D000465:Algorithms; D000818:Animals; D001483:Base Sequence / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D030561:Databases, Nucleic Acid; D006801:Humans; D053124:Influenza A Virus, H5N1 Subtype / Q000235:genetics; D010802:Phylogeny; D012333:RNA, Messenger / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid
D012333:RNA, Messenger