Classification analysis of triplet periodicity in protein-coding regions of genes.
We introduce a new concept of triplet periodicity class (TPC) and a measure of similarity between such classes. We performed classification of 472288 triplet periodicity (TP) regions found in 578868 genes from 29th release of KEGG databank. Totally 2520 classes were obtained. They contain 94% of 472288 found cases of TP. For 92% of TP regions contained in classes the same linkage of TP to open reading frame (ORF) is observed. For 8% of TP cases we revealed a shift between ORF of a gene and ORF common for majority of genes contained in a TPC. For these 8% of periodic regions the hypothetical amino acid sequences corresponding to ORF built by TPC were made. BLAST program has shown that 2679 hypothetical amino acid sequences have statistically significant similarity with proteins from UniProt databank. We suppose that 8% of TP regions contained in classes possess a mutation originating from ORF shift. Obtained TPCs can be used for identification of genes' coding regions as well as for searching for mutations arisen arising from ORF shift.
Frenkel
F E
FE
Bioengineering Centre of RAS, Moscow, Russia. felix.frenkel@gmail.com
Korotkov
E V
EV
D000465:Algorithms; D000595:Amino Acid Sequence; D001483:Base Sequence; D002965:Classification / Q000379:methods; D005796:Genes; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D011506:Proteins / Q000737:chemistry / Q000235:genetics*; D017422:Sequence Analysis, DNA; D020539:Sequence Analysis, Protein
D011506:Proteins