?url_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Adc&rft.title=Seven+clusters+in+genomic+triplet+distributions&rft.creator=Gorban%2C+Prof.+Alexander+N.&rft.creator=Zinovyev%2C+Dr.+Andrei+Yu&rft.creator=Popova%2C+Dr.+Tatyana+G.&rft.subject=Theoretical+Biology&rft.description=+++Motivation%3A+In+several+recent+papers+new+algorithms+were+proposed+for+detecting+coding+regions+without+requiring+learning+dataset+of+already+known+genes.+In+this+paper+we+studied+cluster+structure+of+several+genomes+in+the+space+of+codon+usage.+This+allowed+to+interpret+some+of+the+results+obtained+in+other+studies+and+propose+a+simpler+method%2C+which+is%2C+nevertheless%2C+fully%0Afunctional.++%0A+++Results%3A+Several+complete+genomic+sequences+were+analyzed%2C+using+visualization+of+tables+of+triplet+counts+in+a+sliding+window.+The+distribution+of+64-dimensional+vectors+of+triplet+frequencies+displays+a+well-detectable+cluster+structure.+The+structure+was+found+to+consist+of+seven+clusters%2C+corresponding+to+protein-coding+information+in+three+possible+phases+in+one+of+the+two+complementary+strands+and+in+the+non-coding+regions.+Awareness+of+the+existence+of+this+structure+allows+development+of+methods+for+the+segmentation+of+sequences+into+regions+with+the+same+coding+phase+and+non-coding+regions.%0A+++This+method+may+be+completely+unsupervised+or+use+some+external+information.+Since+the+method+does+not+need+extraction+of+ORFs%2C+it+can+be+applied+even+for+unassembled+genomes.+Accuracy+calculated+on+the+base-pair+level+(both+sensitivity+and+specificity)+exceeds+90%25.+This+is+not+worse+as+compared+to+such+methods+as+HMM%2C+however%2C+has+the+advantage+to+be+much+simpler+and+clear.%0A&rft.date=2002&rft.type=Preprint&rft.type=NonPeerReviewed&rft.format=application%2Fpdf&rft.identifier=http%3A%2F%2Fcogprints.org%2F3077%2F1%2FSeven.pdf&rft.identifier=++Gorban%2C+Prof.+Alexander+N.+and+Zinovyev%2C+Dr.+Andrei+Yu+and+Popova%2C+Dr.+Tatyana+G.++(2002)+Seven+clusters+in+genomic+triplet+distributions.++%5BPreprint%5D+++++&rft.relation=http%3A%2F%2Fcogprints.org%2F3077%2F