INPUT SEQUENCE (A) : data/2HA9.code INPUT SEQUENCE (B) : data/target_ASTRAL.code SUBSEQUENCE OPTION : Whole sequence comparison EXEC OPTION : Naive Dynamic Programing RATIO : lcs/trimmed_seq_a = 0.545 (= 214/ 393), lcs/trimmed_seq_b = 0.663 (= 214/ 323) SEQ A : name = ./PDBdata/2HA9.pdb c1 SEQ A : residue = ADIRQVTETIAIEEQNFDIRTITGISLLDCIDPDINRAAEKIYQKITTKAANLVAVGDEIAAELGIPIVNKRVSVTPISLIGAATDATDYVVLAKALDKAAKEIGVDFIGGFSALVQKGYQKGDEILINSIPRALAETDKVCSSVNIGSTKSGINTAVADGRIIKETANLSDGVAKLVVFANAVEDNPFAAFHGVGEADVIINVGVSGPGVVKRALEKVRGQSFDVVAETVKKTAFKITRIGQLVGQASERLGVEFGIVDLSLAPTDSVARVLEEGLETVGTHGTTAALALLNDQVKKGGVACNDEGIAAVQNGSLNLEKLEATAICSDIAIPEDTPAETIAAIADEAAIGVINKTTAVRIIPKGKEGDIEFTAPVKVNGASSVDFISRGGQIPAPI SEQ A : code = --QAAAAAABBJOG0000OR000000RQAB00QGQAAAAAAAAAAAAAABQ3QAAAAAAAAAABR000R0000000OQAAAAABGR0R0RQAAAAAAAAAAAAB00R0010RG0R1QB00001HAAAAABAAAAAA8G00000000000QB0000QAAABQAAAAAAAI80PIQABG0000R00QB00ORG0000RG0R000000001QAAAAAAAAAG0R00QAAAAAAAAAAAAAAAAAAAAAAAAAAABRG00000000000PJ0QAAAABR30R01BG0RQAAAAAAAAAAAAAABQB0O229AAAAHBRRG0QAAAABRR00000000QB00QAAAAAAAAAAAAAAB0000000000000R0000O3000300RO0RQAAAAB000000-- SEQ A : lcs = ---------------------------------------AAAAAAAAAA----AAAAAAAAAABR000-0000000--------GR-R0RQ------------B00-00-0--0--QB0000----AAA-AAAAAA--00000000000--0---Q---B-----------------0000R00--0--RG000-R-0-0000000--------------R--Q------AAAAAAAAAAAAAAAAAAAAABR-00000000000--0QAAAAB--0---BG0-QAAAAAAAAA-----B--0----------RRG0Q----BR-00000000QB00QAAAAAAAAAAAAAAB000000000----R0000--000-------QAAAA-00------ SEQ B : name = ./pdbstyle-1.71/2a/d12asa_.ent c1 SEQ B : residue = AYIAKQRQISFVKSHFSRQLEERLGLIEVQAPILSRVGDGTQDNLSGAEKAVQVKVKALPDAQFEVVHSLAKWKRQTLGQHDFSAGEGLYTHMKALRPDEDRLSPLHSVYVDQWDWERVMGDGERQFSTLKSTVEAIWAGIKATEAAVSEEFGLAPFLPDQIHFVHSQELLSRYPDLDAKGRERAIAKDLGAVFLVGIGGKLSDGHRHDVRAPDYDDWSTPSELGHAGLNGDILVWNPVLEDAFELSSMGIRVDADTLKHQLALTGDEDRLELEWHQALLRGEMPQTIGGGIGQSRLTMLLLQLPHIGQVQAGVWPAAVRESVPSLL SEQ B : code = --AAAAAAAAAAAAAAAAAAAAB0R0000000RG000PGRRGRR0RQBG0000000QABQBG00000R0RQAAAAAAAAABR000RG0000R00000QB0R000R000RG000R00000000RRRGQAAAAAAAAAAAAAAAAAAAAAB1BBR000000R000000QAAAAAB0QBG0QAAAAAAAAAB0R00R00000000RGRG0R00003G000RG000QBRG00RG0000000QABRG000000000000QAAAAAAAAABR0QAAABGQAAAAAABRRG000000000QAAAAAAABR0R0QAABG00000QAAAA0G0R-- SEQ B : lcs = --AAAAAAAAAAAAAAAAAAAAB-R0000000--000----GRR0RQB-000000-Q-B---0000-----AAAAAAAAA--000--0000-00000QB0-000R000RG000R00000000R---QAAAAAAAAAAAAAAAAAAAAAB---R000000-000000QAAAA-B0-BG0QAAAAAAAAAB0R--R------------------------G0--QBR-00--000000-Q-B------------00QAAAAAAAAA-----------AAAAAB---000000000---------R0-0-----00000QAAAA0-0--- RATIO : lcs/trimmed_seq_a = 0.242 (= 95/ 393), lcs/trimmed_seq_b = 0.896 (= 95/ 106) SEQ A : name = ./PDBdata/2HA9.pdb c1 SEQ A : residue = ADIRQVTETIAIEEQNFDIRTITGISLLDCIDPDINRAAEKIYQKITTKAANLVAVGDEIAAELGIPIVNKRVSVTPISLIGAATDATDYVVLAKALDKAAKEIGVDFIGGFSALVQKGYQKGDEILINSIPRALAETDKVCSSVNIGSTKSGINTAVADGRIIKETANLSDGVAKLVVFANAVEDNPFAAFHGVGEADVIINVGVSGPGVVKRALEKVRGQSFDVVAETVKKTAFKITRIGQLVGQASERLGVEFGIVDLSLAPTDSVARVLEEGLETVGTHGTTAALALLNDQVKKGGVACNDEGIAAVQNGSLNLEKLEATAICSDIAIPEDTPAETIAAIADEAAIGVINKTTAVRIIPKGKEGDIEFTAPVKVNGASSVDFISRGGQIPAPI SEQ A : code = --QAAAAAABBJOG0000OR000000RQAB00QGQAAAAAAAAAAAAAABQ3QAAAAAAAAAABR000R0000000OQAAAAABGR0R0RQAAAAAAAAAAAAB00R0010RG0R1QB00001HAAAAABAAAAAA8G00000000000QB0000QAAABQAAAAAAAI80PIQABG0000R00QB00ORG0000RG0R000000001QAAAAAAAAAG0R00QAAAAAAAAAAAAAAAAAAAAAAAAAAABRG00000000000PJ0QAAAABR30R01BG0RQAAAAAAAAAAAAAABQB0O229AAAAHBRRG0QAAAABRR00000000QB00QAAAAAAAAAAAAAAB0000000000000R0000O3000300RO0RQAAAAB000000-- SEQ A : lcs = --------------0000O-000000R---00--------------------------------R---R000000-------------------------------R001-----1--00-----------------G000000000-----------------------------G0000-00--0--R-0000RG0---------1Q------------------------------------------B-G00000000000--0--------0R-----R------------------0--------------QA---B-------------------------------------000000R0000--------R----------00000-- SEQ B : name = ./pdbstyle-1.71/2c/d32c2a1.ent c1 SEQ B : residue = DIVLTQSPASLAVSLGQRATISCRASKSVSTSGYGYMHWNQQKPGQPPRLLIYLVSNLESGVPARFSGSGSGTDFTLNIHPVEEEDAATYYCQHIREPLTFGGGTKLEIK SEQ B : code = --00000O000000R00RR000000R0018100RG00000000R0G0000000RR0000RG01QBG00000R00000000RR0QABGG0000001R1R0000R00000-- SEQ B : lcs = ---0000O000000R00RR000000R001-100-G00000000-0G0000000R-0000RG01QBG00000-00000000RR0QAB--000000-R--0000R00000-- ...... ...... ...... RATIO : lcs/trimmed_seq_a = 0.254 (= 100/ 393), lcs/trimmed_seq_b = 0.833 (= 100/ 120) SEQ A : name = ./PDBdata/2HA9.pdb c1 SEQ A : residue = ADIRQVTETIAIEEQNFDIRTITGISLLDCIDPDINRAAEKIYQKITTKAANLVAVGDEIAAELGIPIVNKRVSVTPISLIGAATDATDYVVLAKALDKAAKEIGVDFIGGFSALVQKGYQKGDEILINSIPRALAETDKVCSSVNIGSTKSGINTAVADGRIIKETANLSDGVAKLVVFANAVEDNPFAAFHGVGEADVIINVGVSGPGVVKRALEKVRGQSFDVVAETVKKTAFKITRIGQLVGQASERLGVEFGIVDLSLAPTDSVARVLEEGLETVGTHGTTAALALLNDQVKKGGVACNDEGIAAVQNGSLNLEKLEATAICSDIAIPEDTPAETIAAIADEAAIGVINKTTAVRIIPKGKEGDIEFTAPVKVNGASSVDFISRGGQIPAPI SEQ A : code = --QAAAAAABBJOG0000OR000000RQAB00QGQAAAAAAAAAAAAAABQ3QAAAAAAAAAABR000R0000000OQAAAAABGR0R0RQAAAAAAAAAAAAB00R0010RG0R1QB00001HAAAAABAAAAAA8G00000000000QB0000QAAABQAAAAAAAI80PIQABG0000R00QB00ORG0000RG0R000000001QAAAAAAAAAG0R00QAAAAAAAAAAAAAAAAAAAAAAAAAAABRG00000000000PJ0QAAAABR30R01BG0RQAAAAAAAAAAAAAABQB0O229AAAAHBRRG0QAAAABRR00000000QB00QAAAAAAAAAAAAAAB0000000000000R0000O3000300RO0RQAAAAB000000-- SEQ A : lcs = -------------------R000000----0----------------------------------000-0000000-QA----B--0R0R---------------0R00-0R-0----00------AAABA------G------00000QB0---QAAA--AAA-----------B-----R---------------------00001------------R00Q-------------------------AAB-G00000000000--0--------0R0---0-QAAAA--------------------------G-Q----BR---------Q----A-------------B------------------------------QA------------ SEQ B : name = ./zy/d1zyma2.ent c1 SEQ B : residue = SGILASPGIAFGKALLLKEKIIDLSAIQDEVILVAADLTPSETAQLNLKKVLGFITDAGGRTSHTSIMARSLELPAIVGTGSVTSQVKNDDYLILDAVNNQVYVNPTNEVIDKMRAVQEQVASE SEQ B : code = --R0R0000000000000PJ000QAB0R0R0R000R000QAHAABGRQAGGR0000R0R1QB0QAAAAHAABR00001R0R0QAABG00R000000QBR00000R00QAAAAGQB1RQABQA-- SEQ B : lcs = --R0-0000000000000--000QAB0R0R0R000R000-A-AAB---AG--0000-0--QB0QAAAA-AABR00001R0-0QAABG00-000000---00000R00QAAAAGQB-RQABQA-- RATIO TABLE : range | frequency RATIO TABLE : --------------|-------------- RATIO RABLE : [0.9, 1.0] | 4 RATIO TABLE : [0.8, 0.9) | 21 RATIO TABLE : [0.7, 0.8) | 132 RATIO TABLE : [0.6, 0.7) | 511 RATIO TABLE : [0.5, 0.6) | 1308 RATIO TABLE : [0.4, 0.5) | 2000 RATIO TABLE : [0.3, 0.4) | 2705 RATIO TABLE : [0.2, 0.3) | 3857 RATIO TABLE : [0.1, 0.2) | 1946 RATIO TABLE : [0.0, 0.1) | 521 RATIO : lcs/trimmed_seq_a = 0.919 (= 361/ 393), lcs/trimmed_seq_b = 0.288 (= 361/ 1252) SEQ A : name = ./PDBdata/2HA9.pdb c1 SEQ A : residue = ADIRQVTETIAIEEQNFDIRTITGISLLDCIDPDINRAAEKIYQKITTKAANLVAVGDEIAAELGIPIVNKRVSVTPISLIGAATDATDYVVLAKALDKAAKEIGVDFIGGFSALVQKGYQKGDEILINSIPRALAETDKVCSSVNIGSTKSGINTAVADGRIIKETANLSDGVAKLVVFANAVEDNPFAAFHGVGEADVIINVGVSGPGVVKRALEKVRGQSFDVVAETVKKTAFKITRIGQLVGQASERLGVEFGIVDLSLAPTDSVARVLEEGLETVGTHGTTAALALLNDQVKKGGVACNDEGIAAVQNGSLNLEKLEATAICSDIAIPEDTPAETIAAIADEAAIGVINKTTAVRIIPKGKEGDIEFTAPVKVNGASSVDFISRGGQIPAPI SEQ A : code = --QAAAAAABBJOG0000OR000000RQAB00QGQAAAAAAAAAAAAAABQ3QAAAAAAAAAABR000R0000000OQAAAAABGR0R0RQAAAAAAAAAAAAB00R0010RG0R1QB00001HAAAAABAAAAAA8G00000000000QB0000QAAABQAAAAAAAI80PIQABG0000R00QB00ORG0000RG0R000000001QAAAAAAAAAG0R00QAAAAAAAAAAAAAAAAAAAAAAAAAAABRG00000000000PJ0QAAAABR30R01BG0RQAAAAAAAAAAAAAABQB0O229AAAAHBRRG0QAAAABRR00000000QB00QAAAAAAAAAAAAAAB0000000000000R0000O3000300RO0RQAAAAB000000-- SEQ A : lcs = --QAAAAAABB--G0000-R000000RQAB00QGQAAAAAAAAAAAAAABQ-QAAAAAAAAAABR000R0000000OQAAAAABGR0R0RQAAAAAAAAAAAAB00R00-0-G0R-QB0000--AAAAABAAAAAA-G00000000000QB0000QAAABQAAAAAAA--0--QABG0000R00QB00--G0000RG0R0000000--QAAAAAAAAAG0R00QAAAAAAAAAAAAAAAAAAAAAAAAAA-BRG00000000000--0QAAAABR-0R0-BG0RQAAAAAAAAAAAAAABQB0----AAAA-BRRG0QAAAABRR00000000QB00QAAAAAAAAAAAAAAB0000000000000R0000--000-00R-0RQAAAAB000000-- SEQ B : name = ./pdbstyle-1.71/mu/d1muka_.ent c1 SEQ B : residue = SSMILTQFGPFIESISGITDQSNDVFEDAAKAFSMFTRSDVYKALDEIPFSDDAMLPIPPTIYTKPSHDSYYYIDALNRVRRKTYQGPDDVYVPNCSIVELLEPHETLTSYGRLSEAIENRAKDGDSQARIATTYGRIAESQARQIKAPLEKFVLALLVAEAGGSLYDPVLQKYDEIPDLSHNCPLWCFREICRHISGPLPDRAPYLYLSAGVFWLMSPRMTSAIPPLLSDLVNLAILQQTAGLDPSLVKLGVQICLHAAASSSYSWFILKTKSIFPQNTLHSMYESLEGGYCPNLEWLEPRSDYKFMYMGVMPLSAKYARSAPSNDKKARELGEKYGLSSVVGELRKRTKTYVKHDFASVRYIRDAMACTSGIFLVRTPTETVLQEYTQSPEIKVPIPQKDWTGPIGEIRILKDTTSSIARYLYRTWYLAAARMAAQPRTWDPLFQAIMRSQYVTARGGSGAALRESLYAINVSLPDFKGLPVKAATKIFQAAQLANLPFSHTSVAILADTSMGLRNQVQRRPRSIMPLNVPQQQVSAPHTLTADYINYHMNLSPTSGSAVIEKVIPLGVYASSPPNQSINIDISACDASITWDFFLSVIMAAIHEGVASSSIGKPFMGVPASIVNDESVVGVRAARPISGMQNMIQHLSKLYKRGFSYRVNDSFSPGNDFTHMTTTFPSGSTATSTEHTANNSTMMETFLTVWGPEHTDDPDVLRLMKSLTIQRNYVCQGDDGLMIIDGTTAGKVNSETIQNDLELISKYGEEFGWKYDIAYDGTAEYLKLYFIFGCRIPNLSRHPIVGKERANSSAEEPWPAILDQIMGVFFNGVHDGLQWQRWIRYSWALCCAFSRQRTMIGESVGYLQYPMWSFVYWGLPLVKAFGSDPWIFSWYMPTGDLGMYSWISLIRPLMTRWMVANGYVTDRCSTVFGNADYRRCFNELKLYQGYYMAQLPRNPKEVREQFTQALSDYLMQNPELKSRVLRGRSEWEKYGAGIIHNPPSLFDVPHKWYQGAQEAAIATREELAEMDETLMRARRHSYSSFSKLLEAYLLVKWRMCEAREPSVDLRLPLCAGIDPLNSDPFLKMVSVGPMLQSTRKYFAQTLFMAKTVSGLDVNAIDSALLRLRTLGADKKALTAQLLMVGLQESEADALAGKIMLQDVNTVQLARVVNLAVPDTWMSLDFDSMFKHHVKLLPKDGRHLNTDIPPRMGWLRAILRFLGAGMVMTATGVAVDIYLEDIHGGGRSLGQRFMTWMRQEGR SEQ B : code = --AAAA0RQAAAAAABRR0000QAAAAAAAAAAABG0QAAAAAAAABGR00QABG0000QAAGG000RAAB0000QBR0000000R0QBRGG00R001QABG000RQBQBG0000QAAAAAAAB00QAAAAAAAAAAAAAAAABRGR00QAAAAAAAAAAAAB00000QABRG00R000QAB0QAAAAAAAAAAAAB0RGRGRGR0000R000000R0QBG0QAAAAAAAAAAAAAAAAA0RR0OQAAAAAAAAAAAAAABGR0QAAAAAA9QBQAAAB0QAG0RRG0O00000000000RQABR00000000000QAB00RG00RQAAAAAAAAABRGQAAAAAAAAAAABGRG00QAAAAAAAAAAABG0R0R0000QAAAAAGA1G0000RR0000QABG000R0RG0000QBGRGQAAAAAAAAAAAAAAAABGQAABGQAAAAAAAAABR0RG00RQAAAAAAAAABR0000RR000RG0QBGQAAAAAABQ0G0QAABQAAAB00000000000RG000000000QAAAAABQAAAAAAAAAAB000000R000GQABRRQAAAAAABG1RG00000000RQAAAB0QB00QAAAAAAAAHABGAAB00G00RR00000000RRG0RG0000000QAAAAAAAAAAAAAB00000000QBG0R0000000R000QBGQHOAAAAAAAAAAAAAAAA00QAAAG0R0QAAAAAAABG0QB00G0000RG00000000QB0000QAAAAAAAAAAAAAAAB0R00000000RG000RR0000RRG0000QAAG0QBG000R0R000000PAAAAAAAAAAAAAAAB00RQAAAAAAAAAAAAAARG0000R0RG0000000QAAAAAB0000R00RR000RRG0QB0000QAAAAAAAAB8QAAAAAAAAABRR00RG00R0R0RGRQAAAAAABRQAAAAAAABG0RG012QAAAAAAAAAAAABRGQAAAAAAAAAAAAAAG000QB0QB000QAAAAAAAAAAAAABG000QAAAAAAAAAAAAAABG000000QAAAAAABG0000000000R00QBG0R00RBGQAB0AAAAAAAAB000RG0QAAAAAABGR0R000QBG0QAAAAAAAAAAAABR00QAAAAAAAAAB000QAAAAAAAAAAAB0R001AAAAAABR0000QAAQBGRQAAABG01G0RG0QG000QABG00QABQAAAAAAAAAAAAAAABG000000000000QR0QAAAAAAAAAAAA80-- SEQ B : lcs = --------QAAAAAAB------------------BG0---------------------------000R---0000---00--------------R---QAB-00--Q---G----QA---------------------------------AAAAAAAAAAAA-------AB--------Q---QAAAAAAAAAA--B-R-------000R000000-0--------------------------OQAAAAA---------BGR0--------------------R--------------0RQA-------------------------------------------------------AAAAAAAAAAAB-0-0R000-------G---0---R-----Q-B--------0000------AAAAA-----------B----------AAAAAA----G00-------------0000--000--0------------0--Q--B-----------------------0000QAAA--BQAAAAAAA-------------0-QAB----------G-------0000R--------00Q--------------B00G--------0000R-G0R-0000000QAAAAAAAAA---------------G--------0R00-Q-----AAAAAAAAAAAAAAAA---AAA-----AAAAAAAB-----------RG00000000--0000QAAAA-----------B-R0-------R-0---------------------BG------------------------------0RQAAAAAAAAAAAAAA-----------------------B----------------QB0--------------------AAAABRR---G-----0---QAAAA--BR-----------R-0----------------------------------000--0--000Q-------------B-00-QAAAAAAAAAAAAAAB-000000---------0000000---R00---0-00------0---------000R-0---------R-----Q--------------------------------------------------------------------------------------------------------------AAAAB-000000-------------------------- // [NOTE]: A trimmed sequence is the sequence obtained by removing residues of // irregular 5-tile codes, such as '-', where regular 5-tile codes are // {0, A, R, Q, B, G, 1, O, H, 3, J, 8, P, 9, 2, I}. Irregular 5-tile // codes are ommited during the LCS computation and LCSs consist of // regular 5-tile codes only.