[Classification of nucleotide sequences over their frequency dictionaries reveals a relation between the structure of sequences and taxonomy of their bearers].
Classification of 16S RNA sequences over their frequency dictionaries, both real ones, and transformed ones was studied. Two entities were considered to be close each other from the point of view of their structure, if their frequency dictionaries were close, in Eucledian metric. A transformation procedure of a frequency dictionary has been implemented that reveals the peculiarities of information structure of a nucleotide sequence. A comparative study of two classification developed over the real frequency dictionary vs. that one developed over the transformed frequency dictionary was carried out. The strong correlation is revealed between the classification and the taxonomy of 16S RNA bearer. For the classes isolated, the information valuable words were identified. These words are the main factors of a difference between the classes. The frequency dictionaries containing the words of the length 3 exhibit the best correlation between a class and a genus. A genus, as a rule, is included into the same class, and the exclusion are sporadic. A development of hierarchy classification over the transformed frequency dictionaries separated one or two taxonomy groups, as each stage of classification. The unexpectedly frequent, or contrary, unexpectedly rare occurred of words (of the length 3) in entities under consideration make the structure difference between the classes of the nucleotide sequences.
Gorban'
A N
AN
Institute of Computing Modelling of SD of RAS, 660036 Russia, Krasnoyarsk, Akademgorodok. gorban@icm.krasn.ru
Popova
T G
TG
Sadovskiĭ
M G
MG
D001419:Bacteria / Q000145:classification* / Q000235:genetics; D001483:Base Sequence; D004014:Dictionaries as Topic; D008433:Mathematics; D012329:RNA, Bacterial / Q000235:genetics; D012335:RNA, Ribosomal / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000145:classification* / Q000235:genetics
D012329:RNA, Bacterial; D012335:RNA, Ribosomal; D012336:RNA, Ribosomal, 16S