/** * Here is some samples of how to use the functions * @param SequenceAlignmentInterface $sequenceAlignmentManager * @return Response * @throws \Exception */ public function clustalseqalignment(SequenceAlignmentInterface $sequenceAlignmentManager) { set_time_limit(0); // we never know ... $sequenceAlignmentManager->setFilename("data/clustal.txt"); $sequenceAlignmentManager->setFormat("CLUSTAL"); $sequenceAlignmentManager->parseFile(); // You wanna sort your array ? :) $sequenceAlignmentManager->sortAlpha("ASC"); $sequenceAlSort = $sequenceAlignmentManager->getSeqSet(); // You wanna fetch something ? $oOffset13 = $sequenceAlignmentManager->getSeqSet()->offsetGet(13); // You wanna know the longest sequence ? $iMaxLength = $sequenceAlignmentManager->getMaxiLength(); // You wanna know the number of gaps ? $iNumberGaps = $sequenceAlignmentManager->getGapCount(); // Have the same length ? $bIsFlush = $sequenceAlignmentManager->getIsFlush(); // Char at res 10 (10th sequence) $sCharAtRes = $sequenceAlignmentManager->charAtRes(10, 10); // Substring between two residues in a sequence $sSubstrBwRes = $sequenceAlignmentManager->substrBwRes(10,10); // Converts a column number to a residue number in a sequence $iColToRes = $sequenceAlignmentManager->colToRes(10, 50); // Converts a residue number to a column number in a sequence $iResToCol = $sequenceAlignmentManager->resToCol(10, 47); // Creates a new alignment set from index 5 to 10 $sequenceAlignmentManager->subalign(5, 10); $oSubALign = $sequenceAlignmentManager; // Creates a new alignment with selected indexes $sequenceAlignmentManager->select(1,2,3); $oSelectAlign = $sequenceAlignmentManager; // Determines the index position of both variant and invariant residues according // to a given "percentage threshold" similar to that in the consensus() method. $aResVar = $sequenceAlignmentManager->resVar(); // Returns the consensus string for an alignment set $aConsensus = $sequenceAlignmentManager->consensus(); // Adding a new sequence object $sequenceAlignmentManager->addSequence($oOffset13); $sequenceAlignmentManagerAdd = $sequenceAlignmentManager; // Dropping a sequence $sequenceAlignmentManager->deleteSequence("sp|P04637|P53_HUMAN"); $sequenceAlignmentManagerDel = $sequenceAlignmentManager; return $this->render('default/clustalseqalignment.html.twig', [ 'sequenceAlSort' => $sequenceAlSort, 'offset13' => $oOffset13, 'maxLength' => $iMaxLength, 'numberGaps' => $iNumberGaps, 'isFlush' => $bIsFlush, 'sCharAtRes' => $sCharAtRes, 'sSubstrBwRes' => $sSubstrBwRes, 'colToRes' => $iColToRes, 'resToCol' => $iResToCol, 'subALign' => $oSubALign, 'selectAlign' => $oSelectAlign, 'resVar' => $aResVar, 'consensus' => $aConsensus, 'sequenceAlignmentManagerAdd' => $sequenceAlignmentManagerAdd, 'sequenceAlignmentManagerDel' => $sequenceAlignmentManagerDel ] ); }
Sort sequences :
ArrayIterator {#680 : false : false : array:34 [ 0 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#653 -primAcc: "sp|O09185|P53_CRIGR" -entryName: null -seqLength: 426 -start: 0 -end: 425 -molType: null -date: null -source: null -sequence: "MEEPQSDLSIEL-PLSQETFSDLWKLLPPNNVLSTLPS-SDSIEE-LFLSENVTGWLEDSGGALQGVAAAA---ASTAEDPVTET-------PAPVASAPATPWPLSSSVPSYKTYQGDYGFRLGFLHSGTAKSVTCTYSPSLNKLFCQLAKTCPVQLWVNSTPPPGTRVRAMAIYKKLQYMTEVVRRCPHHERSSE-GDSLAPPQHLIRVEGNLHAEYLDDKQTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDPSGNLLGRNSFEVRICACPGRDRRTEEKNFQKKGEPCPELP---PKSAKRALPT--NTS--SSPP-PK-----KKTLDGEYFTLKIRGHERFKMFQELNEALELKDAQASKGSEDNGAHSSYL-----KSKKGQSASRLKKLMIKREGPDSD-" -description: null -organism: null -fragment: null } 1 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#669 -primAcc: "sp|O12946|P53_PLAFE" -entryName: null -seqLength: 426 -start: 0 -end: 425 -molType: null -date: null -source: null -sequence: "MMDEQGLDGMQILPGSQDSFSELWASVQTPSIATI---------AEEF-------------DD---H---LGNLLQNGFDMNLFE-------LPPEMVAKDSVTPPSSTVPVVTDYPGEYGFQLRFQKSGTAKSVTSTFSELLKKLYCQLAKTSPVEVLLSKEPPQGAVLRATAVYKKTEHVADVVRRCPHHQT----EDTAEHRSHLIRLEGSQRALYFEDPHTKRQSVTVPYEPPQLGSETTAILLSFMCNSSCMGGMNRRQILTILTLETPDGLVLGRRCFEVRVCACPGRDRKTDEESSTKTPNGPKQTK-------KRKQAPSNSAPHTT-TVMKSKSSSSAEEEDKEVFTVLVKGRERYEIIKKINEAFEGAAEKEKAKN------------KVAVKQELPVPSSGKRLVQRGERSDSD-" -description: null -organism: null -fragment: null } 2 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#664 -primAcc: "sp|O36006|P53_MARMO" -entryName: null -seqLength: 426 -start: 0 -end: 425 -molType: null -date: null -source: null -sequence: "MEEAQSDLSIEP-PLSQETFSDLWNLLPENNVLSPVLS-PPM-DDLLLSSEDVENWFDK--GPDEAL---QMSAAPAPKAPTPAA-------STLAAPSPATSWPLSSSVPSQNTYPGVYGFRLGFLHSGTAKSVTCTYSPSLNKLFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKKSQHMTEVVRRCPHHERCSD-SDGLAPPQHLIRVEGNLRAEYLDDRNTFRHSVVVPYEPPEVGSECTTIHYNYMCNSSCMGGMNRRPILTIITLEGSSGNLLGRNSFEVRVCACPGRDRRTEEENFRKRGEPCPEPP---PRSTKRALPN--GTS--SSPQ-PK-----KKPLDGEYFTLKIRGRARFEMFQELNEALELKDAQAEKEPGESRPHPSYL-----KSKKGQSTSRHKKIIFKREGPDSD-" -description: null -organism: null -fragment: null } 3 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#679 -primAcc: "sp|O57538|P53_XIPHE" -entryName: null -seqLength: 426 -start: 0 -end: 425 -molType: null -date: null -source: null -sequence: "-ME----EADLTLPLSQDTFHDLWNNVFLSTEN--------------------ESLAPPE--G---L---LSQ------NMDFWE--------DPETMQETKNVPTAPTVPAISNYAGEHGFNLEFNDSGTAKSVTSTYSVKLGKLFCQLAKTTPIGVLVKEEPPQGAVIRATSVYKKTEHVGEVVKRCPHHQS----EDLSDNKSHLIRVEGSQLAQYFEDPNTRRHSVTVPYERPQLGSEMTTILLSFMCNSSCMGGMNRRPILTILTLETTEGEVLGRRCFEVRVCACPGRDRKTEEGNLEK--SGTKQTK-------KRKSAP---APDTS-TAKKSKSASSGEDEDKEIYTLSIRGRNRYLWFKSLNDGLELMDKTG-----------------PKIKQEIPAPSSGKRLLKGGSDSD---" -description: null -organism: null -fragment: null } 4 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#660 -primAcc: "sp|O93379|P53_ICTPU" -entryName: null -seqLength: 426 -start: 0 -end: 425 -molType: null -date: null -source: null -sequence: "MEGNGERDTMMVEPPDSQEFAELWLRN--------------------LIVRDNSLWGKEEEIPDDLQ---E---VPCD-----VL-------LSDMLQPQSSSSPPTSTVPVTSDYPGLLNFTLHFQESSGTKSVTCTYSPDLNKLFCQLAKTCPVLMAVSSSPPPGSVLRATAVYKRSEHVAEVVRRCPHHERSNDSSDGPAPPGHLLRVEGNSRAVYQEDGNTQAHSVVVPYEPPQVGSQSTTVLYNYMCNSSCMGGMNRRPILTIITLETQDGHLLGRRTFEVRVCACPGRDRKTEESNFKKQQEPKTSGK---T-LTKRSMKD--PPSHPEASKKSK-----NSSSDDEIYTLQVRGKERYEFLKKINDGLELSDVVPPADQEKYRQKLLSKTCRKERDGAAGEPKRGKKRLVKEEKCDSD-" -description: null -organism: null -fragment: null } 5 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#666 -primAcc: "sp|P02340|P53_MOUSE" -entryName: null -seqLength: 426 -start: 0 -end: 425 -molType: null -date: null -source: null -sequence: "MEESQSDISLEL-PLSQETFSGLWKLLPPEDILPS-----PHCMDDLLLPQDVEEFFEG---PSEAL---RVSGAPAAQDPVTET-------PGPVAPAPATPWPLSSFVPSQKTYQGNYGFHLGFLQSGTAKSVMCTYSPPLNKLFCQLAKTCPVQLWVSATPPAGSRVRAMAIYKKSQHMTEVVRRCPHHERCSD-GDGLAPPQHLIRVEGNLYPEYLEDRQTFRHSVVVPYEPPEAGSEYTTIHYKYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRDSFEVRVCACPGRDRRTEEENFRKKEVLCPELP---PGSAKRALPT--CTS--ASPP-QK-----KKPLDGEYFTLKIRGRKRFEMFRELNEALELKDAHATEESGDSRAHSSYL-----KTKKGQSTSRHKKTMVKKVGPDSD-" -description: null -organism: null -fragment: null } 6 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#659 -primAcc: "sp|P04637|P53_HUMAN" -entryName: null -seqLength: 426 -start: 0 -end: 425 -molType: null -date: null -source: null -sequence: "MEEPQSDPSVEP-PLSQETFSDLWKLLPENNVLSPLPS-QA-MDDLMLSPDDIEQWFTEDPGPDEAP---RMPEAAPPVAPAPAA-------PTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSD-SDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELP---PGSTKRALPN--NTS--SSPQ-PK-----KKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPGGSRAHSSHL-----KSKKGQSTSRHKKLMFKTEGPDSD-" -description: null -organism: null -fragment: null } 7 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#677 -primAcc: "sp|P07193|P53_XENLA" -entryName: null -seqLength: 426 -start: 0 -end: 425 -molType: null -date: null -source: null -sequence: "-MEPSSETGMDP-PLSQETFEDLWSLLPDPLQTVTCR------------LDNLSEFPDY------PL-AADMT-----------V-------LQEGLMGNAVPTVTSCAVPSTDDYAGKYGLQLDFQQNGTAKSVTCTYSPELNKLFCQLAKTCPLLVRVESPPPRGSILRATAVYKKSEHVAEVVKRCPHHERSVEPGEDAAPPSHLMRVEGNLQAYYMEDVNSGRHSVCVPYEGPQVGTECTTVLYNYMCNSSCMGGMNRRPILTIITLETPQGLLLGRRCFEVRVCACPGRDRRTEEDNYTKKRGLKPSG--------KRELAH--PPS--SEPPLPK-KRLVVVDDDEEIFTLRIKGRSRYEMIKKLNDALELQESLDQQK--------VTIKCR--KCRDEIKPKKGKKLLVKDEQPDSE-" -description: null -organism: null -fragment: null } 8 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#650 -primAcc: "sp|P10360|P53_CHICK" -entryName: null -seqLength: 426 -start: 0 -end: 425 -molType: null -date: null -source: null -sequence: "MAE-----EMEPLLEPTEVFMDLWSMLPY-------------SMQQLPLPEDHSNWQELSPLEPSDP---PPPPPPPPLPLAAAA-------PPPLNPPTPPRAAPSPVVPSTEDYGGDFDFRVGFVEAGTAKSVTCTYSPVLNKVYCRLAKPCPVQVRVGVAPPPGSSLRAVAVYKKSEHVAEVVRRCPHHERCGGGTDGLAPAQHLIRVEGNPQARYHDDETTKRHSVVVPYEPPEVGSDCTTVLYNFMCNSSCMGGMNRRPILTILTLEGPGGQLLGRRCFEVRVCACPGRDRKIEEENFRKRGGAG--------GVAKRAMSP--PTEA-PEPPKKR-----VLNPDNEIFYLQVRGRRRYEMLKEINEALQLAEGGSAPRPSKGRR----------VKVEGPQPSCGKKLLQKGSD-----" -description: null -organism: null -fragment: null } 9 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#672 -primAcc: "sp|P10361|P53_RAT" -entryName: null -seqLength: 426 -start: 0 -end: 425 -molType: null -date: null -source: null -sequence: "MEDSQSDMSIEL-PLSQETFSCLWKLLPPDDILPTTATGSPNSMEDLFLPQDVAELLEG---PEEAL---QVS-APAAQEPGTEA-------PAPVAPASATPWPLSSSVPSQKTYQGNYGFHLGFLQSGTAKSVMCTYSISLNKLFCQLAKTCPVQLWVTSTPPPGTRVRAMAIYKKSQHMTEVVRRCPHHERCSD-GDGLAPPQHLIRVEGNPYAEYLDDRQTFRHSVVVPYEPPEVGSDYTTIHYKYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRDSFEVRVCACPGRDRRTEEENFRKKEEHCPELP---PGSAKRALPT--STS--SSPQ-QK-----KKPLDGEYFTLKIRGRERFEMFRELNEALELKDARAAEESGDSRAHSSYP-----KTKKGQSTSRHKKPMIKKVGPDSD-" -description: null -organism: null -fragment: null } 10 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#652 -primAcc: "sp|P13481|P53_CHLAE" -entryName: null -seqLength: 426 -start: 0 -end: 425 -molType: null -date: null -source: null -sequence: "MEEPQSDPSIEP-PLSQETFSDLWKLLPENNVLSPLPS-QA-VDDLMLSPDDLAQWLTEDPGPDEAP---RMSEAAPHMAPTPAA-------PTPAAPAPAPSWPLSSSVPSQKTYHGSYGFRLGFLHSGTAKSVTCTYSPDLNKMFCQLAKTCPVQLWVDSTPPPGSRVRAMAIYKQSQHMTEVVRRCPHHERCSD-SDGLAPPQHLIRVEGNLRVEYSDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENFRKKGEPCHELP---PGSTKRALPN--NTS--SSPQ-PK-----KKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPAGSRAHSSHL-----KSKKGQSTSRHKKFMFKTEGPDSD-" -description: null -organism: null -fragment: null } 11 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#667 -primAcc: "sp|P25035|P53_ONCMY" -entryName: null -seqLength: 426 -start: 0 -end: 425 -molType: null -date: null -source: null -sequence: "MADLAEN---VSLPLSQESFEDLWKMNLNLVAV---------------QPPETESWVGYDNFMMEAP-------LQVEFDPSLFEVSATEPAPQPSISTLDTGSPPTSTVPTTSDYPGALGFQLRFLQSSTAKSVTCTYSPDLNKLFCQLAKTCPVQIVVDHPPPPGAVVRALAIYKKLSDVADVVRRCPHHQSTSENNEGPAPRGHLVRVEGNQRSEYMEDGNTLRHSVLVPYEPPQVGSECTTVLYNFMCNSSCMGGMNRRPILTIITLETQEGQLLGRRSFEVRVCACPGRDRKTEEINLKKQQETTLETKTKPAQGIKRAMKE-ASLPA-PQPGASKKTKSSPAVSDDEIYTLQIRGKEKYEMLKKFNDSLELSELVPVADADKYRQKCLTKRVA--KRDFGVGPKKRKKLLVKEEKSDSD-" -description: null -organism: null -fragment: null } 12 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#657 -primAcc: "sp|P41685|P53_FELCA" -entryName: null -seqLength: 426 -start: 0 -end: 425 -molType: null -date: null -source: null -sequence: "MQEPPLELTIEP-PLSQETFSELWNLLPENNVLSSELS-SAM--NELPLSEDVANWLDE--APDDAS---GMSAVPAPAAPAP------------ATPAPAISWPLSSFVPSQKTYPGAYGFHLGFLQSGTAKSVTCTYSPPLNKLFCQLAKTCPVQLWVRSPPPPGTCVRAMAIYKKSEFMTEVVRRCPHHERCPDSSDGLAPPQHLIRVEGNLHAKYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNFMCNSSCMGGMNRRPIITIITLEDSNGKLLGRNSFEVRVCACPGRDRRTEEENFRKKGEPCPEPP---PGSTKRALPP--STS--STPP-QK-----KKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQSGKEPGGSRAHSSHL-----KAKKGQSTSRHKKPMLKREGLDSD-" -description: null -organism: null -fragment: null } 13 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#673 -primAcc: "sp|P51664|P53_SHEEP" -entryName: null -seqLength: 426 -start: 0 -end: 425 -molType: null -date: null -source: null -sequence: "MEESQAELGVEP-PLSQETFSDLWNLLPENNLLSSELS-AP-VDDLLPYSEDVVTWLDE--CPNEAP---QMPEPPAQA-----------------ALAPATSWPLSSFVPSQKTYPGNYGFRLGFLHSGTAKSVTCTYSPSLNKLFCQLAKTCPVQLWVDSPPPPGTRVRAMAIYKKLEHMTEVVRRSPHHERSSDYSDGLAPPQHLIRVEGNLRAEYFDDRNTFRHSVVVPYESPEIESECTTIHYNFMCNSSCMGGMNRRPILTIITLEDSRGNLLGRSSFEVRVCACPGRDRRTEEENFRKKGQSCPEPP---PGSTKRALPS--STS--SSPQ-QK-----KKPLDGEYFTLQIRGRKRFEMFRELNEALELMDAQAGREPGESRAHSSHL-----KSKKGPSPSCHKKPMLKREGPDSD-" -description: null -organism: null -fragment: null } 14 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#661 -primAcc: "sp|P56423|P53_MACFA" -entryName: null -seqLength: 426 -start: 0 -end: 425 -molType: null -date: null -source: null -sequence: "MEEPQSDPSIEP-PLSQETFSDLWKLLPENNVLSPLPS-QA-VDDLMLSPDDLAQWLTEDPGPDEAP---RMSEAAPPMAPTPAA-------PTPAAPAPAPSWPLSSSVPSQKTYHGSYGFRLGFLHSGTAKSVTCTYSPDLNKMFCQLAKTCPVQLWVDSTPPPGSRVRAMAIYKQSQHMTEVVRRCPHHERCSD-SDGLAPPQHLIRVEGNLRVEYSDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENFRKKGEPCHQLP---PGSTKRALPN--NTS--SSPQ-PK-----KKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPAGSRAHSSHL-----KSKKGQSTSRHKKFMFKTEGPDSD-" -description: null -organism: null -fragment: null } 15 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#663 -primAcc: "sp|P56424|P53_MACMU" -entryName: null -seqLength: 426 -start: 0 -end: 425 -molType: null -date: null -source: null -sequence: "MEEPQSDPSIEP-PLSQETFSDLWKLLPENNVLSPLPS-QA-VDDLMLSPDDLAQWLTEDPGPDEAP---RMSEAAPPMAPTPAA-------PTPAAPAPAPSWPLSSSVPSQKTYHGSYGFRLGFLHSGTAKSVTCTYSPDLNKMFCQLAKTCPVQLWVDSTPPPGSRVRAMAIYKQSQHMTEVVRRCPHHERCSD-SDGLAPPQHLIRVEGNLRVEYSDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENFRKKGEPCHQLP---PGSTKRALPN--NTS--SSPQ-PK-----KKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPAGSRAHSSHL-----KSKKGQSTSRHKKFMFKTEGPDSD-" -description: null -organism: null -fragment: null } 16 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#662 -primAcc: "sp|P61260|P53_MACFU" -entryName: null -seqLength: 426 -start: 0 -end: 425 -molType: null -date: null -source: null -sequence: "MEEPQSDPSIEP-PLSQETFSDLWKLLPENNVLSPLPS-QA-VDDLMLSPDDLAQWLTEDPGPDEAP---RMSEAAPPMAPTPAA-------PTPAAPAPAPSWPLSSSVPSQKTYHGSYGFRLGFLHSGTAKSVTCTYSPDLNKMFCQLAKTCPVQLWVDSTPPPGSRVRAMAIYKQSQHMTEVVRRCPHHERCSD-SDGLAPPQHLIRVEGNLRVEYSDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENFRKKGEPCHQLP---PGSTKRALPN--NTS--SSPQ-PK-----KKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPAGSRAHSSHL-----KSKKGQSTSRHKKFMFKTEGPDSD-" -description: null -organism: null -fragment: null } 17 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#648 -primAcc: "sp|P67938|P53_BOSIN" -entryName: null -seqLength: 426 -start: 0 -end: 425 -molType: null -date: null -source: null -sequence: "MEESQAELNVEP-PLSQETFSDLWNLLPENNLLSSELS-AP-VDDLLPYT-DVATWLDE--CPNEAP---QMPEPSAPAAPPP------------ATPAPATSWPLSSFVPSQKTYPGNYGFRLGFLQSGTAKSVTCTYSPSLNKLFCQLAKTCPVQLWVDSPPPPGTRVRAMAIYKKLEHMTEVVRRCPHHERSSDYSDGLAPPQHLIRVEGNLRAEYLDDRNTFRHSVVVPYESPEIDSECTTIHYNFMCNSSCMGGMNRRPILTIITLEDSCGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGQSCPEPP---PRSTKRALPT--NTS--SSPQ-PK-----KKPLDGEYFTLQIRGFKRYEMFRELNDALELKDALDGREPGESRAHSSHL-----KSKKRPSPSCHKKPMLKREGPDSD-" -description: null -organism: null -fragment: null } 18 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#649 -primAcc: "sp|P67939|P53_BOVIN" -entryName: null -seqLength: 426 -start: 0 -end: 425 -molType: null -date: null -source: null -sequence: "MEESQAELNVEP-PLSQETFSDLWNLLPENNLLSSELS-AP-VDDLLPYT-DVATWLDE--CPNEAP---QMPEPSAPAAPPP------------ATPAPATSWPLSSFVPSQKTYPGNYGFRLGFLQSGTAKSVTCTYSPSLNKLFCQLAKTCPVQLWVDSPPPPGTRVRAMAIYKKLEHMTEVVRRCPHHERSSDYSDGLAPPQHLIRVEGNLRAEYLDDRNTFRHSVVVPYESPEIDSECTTIHYNFMCNSSCMGGMNRRPILTIITLEDSCGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGQSCPEPP---PRSTKRALPT--NTS--SSPQ-PK-----KKPLDGEYFTLQIRGFKRYEMFRELNDALELKDALDGREPGESRAHSSHL-----KSKKRPSPSCHKKPMLKREGPDSD-" -description: null -organism: null -fragment: null } 19 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#654 -primAcc: "sp|P79734|P53_DANRE" -entryName: null -seqLength: 426 -start: 0 -end: 425 -molType: null -date: null -source: null -sequence: "-----------MAQNDSQEFAELWEKNL----IIQPP-------------GGGSCWDIIN---DEEY-------LPGSFDPNFFE-------NVLEEQPQPSTLPPTSTVPETSDYPGDHGFRLRFPQSGTAKSVTCTYSPDLNKLFCQLAKTCPVQMVVDVAPPQGSVVRATAIYKKSEHVAEVVRRCPHHERTPD-GDNLAPAGHLIRVEGNQRANYREDNITLRHSVFVPYEAPQLGAEWTTVLLNYMCNSSCMGGMNRRPILTIITLETQEGQLLGRRSFEVRVCACPGRDRKTEESNFKKDQETKTMAKT--TTGTKRSLVK-ESSSATLRPEGSK-KAKG-SSSDEEIFTLQVRGRERYEILKKLNDSLELSDVVPASDAEKYRQKFMTK--NKKENRESSEPKQGKKLMVKDEGRSDSD" -description: null -organism: null -fragment: null } 20 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#668 -primAcc: "sp|P79820|P53_ORYLA" -entryName: null -seqLength: 426 -start: 0 -end: 425 -molType: null -date: null -source: null -sequence: "------MDPVPDLPESQGSFQELWETVSYPPLETL---------SLPTVNEPTGSWVATGDMF---L---LDQDLSGTFDDKIFD-------IPIEPVPTNEVNPPPTTVPVTTDYPGSYELELRFQKSGTAKSVTSTYSETLNKLYCQLAKTSPIEVRVSKEPPKGAILRATAVYKKTEHVADVVRRCPHHQN----EDSVEHRSHLIRVEGSQLAQYFEDPYTKRQSVTVPYEPPQPGSEMTTILLSYMCNSSCMGGMNRRPILTILTLET-EGLVLGRRCFEVRICACPGRDRKTEEESRQKTQP-----K-------KRKVTPNTS----S-SKRKKSHSSGEEEDNREVFHFEVYGRERYEFLKKINDGLELLEKESKSKN----------------KDSGMVPSSGKKLKSN--------" -description: null -organism: null -fragment: null } 21 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#658 -primAcc: "sp|P79892|P53_HORSE" -entryName: null -seqLength: 426 -start: 0 -end: 425 -molType: null -date: null -source: null -sequence: "---------------------------------------PAV-NN-LLLSPDVVNWLDE--GPDEAP---RMPAAPA-----P------------LAPAPATSWPLSSFVPSQKTYPGCYGFRLGFLNSGTAKSVTCTYSPTLNKLFCQLAKTCPVQLLVSSPPPPGTRVRAMAIYKKSEFMTEVVRRCPHHERCSDSSDGLAPPQHLIRVEGNLRAEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNFMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENFRKKEEPCPEPP---PRSTKRVLSS--NTS--SSPP-QK-----KKPLDGEYFT----------------------------------------------------------------------" -description: null -organism: null -fragment: null } 22 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#665 -primAcc: "sp|Q00366|P53_MESAU" -entryName: null -seqLength: 426 -start: 0 -end: 425 -molType: null -date: null -source: null -sequence: "MEEPQSDLSIEL-PLSQETFSDLWKLLPPNNVLSTLPS-SDSIEE-LFLSENVAGWLEDPGEALQGSAAAAAPAAPAAEDPVAET-------PAPVASAPATPWPLSSSVPSYKTYQGDYGFRLGFLHSGTAKSVTCTYSPSLNKLFCQLAKTCPVQLWVSSTPPPGTRVRAMAIYKKLQYMTEVVRRCPHHERSSE-GDGLAPPQHLIRVEGNMHAEYLDDKQTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDPSGNLLGRNSFEVRICACPGRDRRTEEKNFQKKGEPCPELP---PKSAKRALPT--NTS--SSPQ-PK-----RKTLDGEYFTLKIRGQERFKMFQELNEALELKDAQALKASEDSGAHSSYL-----KSKKGQSASRLKKLMIKREGPDSD-" -description: null -organism: null -fragment: null } 23 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#656 -primAcc: "sp|Q29480|P53_EQUAS" -entryName: null -seqLength: 426 -start: 0 -end: 425 -molType: null -date: null -source: null -sequence: "------------------------------------------------------------------------------------------------------------------------------------------YSPALNKMFCQLAKTCPVYLRISSPPPPGTRVRAMAIYKKSEFMTEVVRRCPHHERCSDSSDGLAPPQHLIRVEGNLRAEYLDDRNTLRHSVVVPYEPPEVGSDCTTIHYNFMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENFRKKEEPCPEPP---PRSTKRVLSS--NTS--SSPP-QK-----EDPLDGEYFTLH--------------------------------------------------------------------" -description: null -organism: null -fragment: null } 24 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#647 -primAcc: "sp|Q29537|P53_CANFA" -entryName: null -seqLength: 426 -start: 0 -end: 425 -molType: null -date: null -source: null -sequence: "MEESQSELNIDP-PLSQETFSELWNLLPENNVLSSELC-PAV-DE-LLLPESVVNWLDE--DSDDAP---RMPATSA-----P------------TAPGPAPSWPLSSSVPSPKTYPGTYGFRLGFLHSGTAKSVTWTYSPLLNKLFCQLAKTCPVQLWVSSPPPPNTCVRAMAIYKKSEFVTEVVRRCPHHERCSDSSDGLAPPQHLIRVEGNLRAKYLDDRNTFRHSVVVPYEPPEVGSDYTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNVLGRNSFEVRVCACPGRDRRTEEENFHKKGEPCPEPP---PGSTKRALPP--STS--SSPP-QK-----KKPLDGEYFTLQIRGRERYEMFRNLNEALELKDAQSGKEPGGSRAHSSHL-----KAKKGQSTSRHKKLMFKREGLDSD-" -description: null -organism: null -fragment: null } 25 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#675 -primAcc: "sp|Q64662|P53_SPEBE" -entryName: null -seqLength: 426 -start: 0 -end: 425 -molType: null -date: null -source: null -sequence: "---------------------DLWNLLPENNVLSPVLS-PPM-DDLLLSSEDVENWFDK--GPDEAL---QMSAAPAPKAPTPAA-------STLAAPTPAISWPLSSSVPSQNTYPGVYGFRLGFIHSGTAKSVTCTYSPSLNKLFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKKSQHMTEVVRRCPHHERCSD-SDGLAPPQHLIRVEGNLRAEYLDDRNTFRHSVVVPYEPPEVGSESTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENFRKRGEPCPEPP---PGSTKRALPT--GTN--SSPQ-PK-----KKPLDGEYFTLKIRGRA---------------------------------------------------------------" -description: null -organism: null -fragment: null } 26 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#655 -primAcc: "sp|Q8SPZ3|P53_DELLE" -entryName: null -seqLength: 426 -start: 0 -end: 425 -molType: null -date: null -source: null -sequence: "MEESQAELGVEP-PLSQETFSDLWKLLPENNLLSSELS-PA-VDDLLLSPEDVANWLDE--RPDEAP---QMPEPPAPAAPTP------------AAPAPATSWPLSSFVPSQKTYPGSYGFHLGFLHSGTAKSVTCTYSPALNKLFCQLAKTCPVQLWVSSPPPPGTRVRAMAIYKKSEYMTEVVRRCPHHERCSDYSDGLAPPQHLIRVEGNLRAEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNFMCNSSCMGGMNRRPILTIITLEDSNGNLLGRNSFEVRVCACPGRDRRTEEENFHKKGQSCPELP---TGSAKRALPT--GTS--SSPP-QK-----KKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPGESRAHSSHL-----KSKKGQSPSRHKKLMFKREGPDSD-" -description: null -organism: null -fragment: null } 27 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#678 -primAcc: "sp|Q92143|P53_XIPMA" -entryName: null -seqLength: 426 -start: 0 -end: 425 -molType: null -date: null -source: null -sequence: "-ME----EADLTLPLSQDTFHDLWNNVFLSTEN--------------------ESLPPPE--G---L---LSQ------NMDFWE--------DPETMQETKNVPTAPTVPAISNYAGEHGFNLEFNDSGTAKSVTSTYSVKLGKLFCQLAKTTPIGVLVKEEPPQGAVIRATAVYKKTEHVGEVVKRCPHHQS----EDLSDNKSHLIRVEGSQLAQYFEDPNTRRHSVTVPYERPQLGSEMTTILLSFMCNSSCMGGMNRRPILTILTLETTEGEVLGRRCFEVRVCACPGRDRKTEEGNLEK--SGTKQTK-------KRKSAP---APDTS-TAKKSKSASSGEDEDKEIYTLSIRGRNRYLWFKSLNDGLELMDKTG-----------------PKIKQEIPAPSSGKRLLKGGSDSD---" -description: null -organism: null -fragment: null } 28 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#671 -primAcc: "sp|Q95330|P53_RABIT" -entryName: null -seqLength: 426 -start: 0 -end: 425 -molType: null -date: null -source: null -sequence: "MEESQSDLSLEP-PLSQETFSDLWKLLPENNLLTTSLN-PPV--DDLLSAEDVANWLNE--DPEEGL---RVPAAPAPEAPAPAA-------PALAAPAPATSWPLSSSVPSQKTYHGNYGFRLGFLHSGTAKSVTCTYSPCLNKLFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKKSQHMTEVVRRCPHHERCSD-SDGLAPPQHLIRVEGNLRAEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENFRKKGEPCPELP---PGSSKRALPT--TTTD-SSPQ-TK-----KKPLDGEYFILKIRGRERFEMFRELNEALELKDAQAEKEPGGSRAHSSYL-----KAKKGQSTSRHKKPMFKREGPDSD-" -description: null -organism: null -fragment: null } 29 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#676 -primAcc: "sp|Q9TTA1|P53_TUPBE" -entryName: null -seqLength: 426 -start: 0 -end: 425 -molType: null -date: null -source: null -sequence: "MEEPQSDPSVEP-PLSQETFSDLWKLLPENNVLSPLPS-QA-MDDLMLSPDDIEQWFTEDPGPDEAP---RMPEAAPPVAPAPAA-------PTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPDLNKLFCQLAKTCPVQLWVDSAPPPGTRVRAMAIYKQSQYVTEVVRRCPHHERCSD-SDGLAPPQHLIRVEGNLHAEYSDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGKLLGRNSFEVRICACPGRDRRTEEENFRKKGESCPKLP---TGSIKRALPT--GSS--SSPQ-PK-----KKPLDEEYFTLQIRGRERFEMLREINEALELKDAMAGKESAGSRAHSSHL-----KSKKGQSTSRHRKLMFKTEGPDSD-" -description: null -organism: null -fragment: null } 30 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#670 -primAcc: "sp|Q9TUB2|P53_PIG" -entryName: null -seqLength: 426 -start: 0 -end: 425 -molType: null -date: null -source: null -sequence: "MEESQSELGVEP-PLSQETFSDLWKLLPENNLLSSELS-LAAVNDLLLSP--VTNWLDE--NPDDAS---RVPAPPAATAPAP------------AAPAPATSWPLSSFVPSQKTYPGSYDFRLGFLHSGTAKSVTCTYSPALNKLFCQLAKTCPVQLWVSSPPPPGTRVRAMAIYKKSEYMTEVVRRCPHHERSSDYSDGLAPPQHLIRVEGNLRAEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNFMCNSSCMGGMNRRPILTIITLEDASGNLLGRNSFEVRVCACPGRDRRTEEENFLKKGQSCPEPP---PGSTKRALPT--STS--SSPV-QK-----KKPLDGEYFTLQIRGRERFEMFRELNDALELKDAQTARESGENRAHSSHL-----KSKKGQSPSRHKKPMFKREGPDSD-" -description: null -organism: null -fragment: null } 31 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#646 -primAcc: "sp|Q9W678|P53_BARBU" -entryName: null -seqLength: 426 -start: 0 -end: 425 -molType: null -date: null -source: null -sequence: "-------------MAESQEFAELWERNL----IST-Q-------------EAGTCWELIN---D-EY-------LPSSFDPNIFD-------NVLTEQPQPSTSPPTASVPVATDYPGEHGFKLGFPQSGTAKSVTCTYSSDLNKLFCQLAKTCPVQMVVNVAPPQGSVIRATAIYKKSEHVAEVVRRCPHHERTPD-GDGLAPAAHLIRVEGNSRALYREDDVNSRHSVVVPYEVPQLGSEFTTVLYNFMCNSSCMGGMNRRPILTIISLETHDGQLLGRRSFEVRVCACPGRDRKTEESNFRKDQETKTLDKI--PSANKRSLTK-DSTSSVPRPEGSK-KAKLSGSSDEEIYTLQVRGKERYEMLKKINDSLELSDVVPPSEMDRYRQKLLTK--GKKKDGQTPEPKRGKKLMVKDEKSDSD-" -description: null -organism: null -fragment: null } 32 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#674 -primAcc: "sp|Q9W679|P53_TETMU" -entryName: null -seqLength: 426 -start: 0 -end: 425 -molType: null -date: null -source: null -sequence: "-ME----EENISLPLSQDTFQDLWDNVSAPPISTI---------QTAAL--ENEAWPAERQMN---M---MCNFMDSTFNEALFN-------LLPEPPSRDGANSSSPTVPVTTDYPGEYGFKLRFQKSGTAKSVTSTYSEILNKLYCQLAKTSLVEVLLGKDPPMGAVLRATAIYKKTEHVAEVVRRCPHHQN----EDSAEHRSHLIRMEGSERAQYFEHPHTKRQSVTVPYEPPQLGSEFTTILLSFMCNSSCMGGMNRRPILTILTLETQEGIVLGRRCFEVRVCACPGRDRKTEETNSTKMQNDAKDAK-------KRKSVP---TPDST-TIKKSKTASSAEEDNNEVYTLQIRGRKRYEMLKKINDGLDLLENKP--KS------------KATHRPDGPIPPSGKRLLHRGEKSDSD-" -description: null -organism: null -fragment: null } 33 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#651 -primAcc: "sp|Q9WUR6|P53_CAVPO" -entryName: null -seqLength: 426 -start: 0 -end: 425 -molType: null -date: null -source: null -sequence: "MEEPHSDLSIEP-PLSQETFSDLWKLLPENNVLSDSLS-PPM-DHLLLSPEEVASWLGENP--DGDG---HVSAAPVSEAPTSAG-------PALVAPAPATSWPLSSSVPSHKPYRGSYGFEVHFLKSGTAKSVTCTYSPGLNKLFCQLAKTCPVQVWVESPPPPGTRVRALAIYKKSQHMTEVVRRCPHHERCSD-SDGLAPPQHLIRVEGNLHAEYVDDRTTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGKLLGRDSFEVRVCACPGRDRRTEEENFRKKGGLCPEPT---PGNIKRALPT--STS--SSPQ-PK-----KKPLDAEYFTLKIRGRKNFEILREINEALEFKDAQTEKEPGESRPHSSYP-----KSKKGQSTSCHKKLMFKREGLDSD-" -description: null -organism: null -fragment: null } ] }
13th sequence
Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#673 -primAcc: "sp|P51664|P53_SHEEP" -entryName: null -seqLength: 426 -start: 0 -end: 425 -molType: null -date: null -source: null -sequence: "MEESQAELGVEP-PLSQETFSDLWNLLPENNLLSSELS-AP-VDDLLPYSEDVVTWLDE--CPNEAP---QMPEPPAQA-----------------ALAPATSWPLSSFVPSQKTYPGNYGFRLGFLHSGTAKSVTCTYSPSLNKLFCQLAKTCPVQLWVDSPPPPGTRVRAMAIYKKLEHMTEVVRRSPHHERSSDYSDGLAPPQHLIRVEGNLRAEYFDDRNTFRHSVVVPYESPEIESECTTIHYNFMCNSSCMGGMNRRPILTIITLEDSRGNLLGRSSFEVRVCACPGRDRRTEEENFRKKGQSCPEPP---PGSTKRALPS--STS--SSPQ-QK-----KKPLDGEYFTLQIRGRKRFEMFRELNEALELMDAQAGREPGESRAHSSHL-----KSKKGPSPSCHKKPMLKREGPDSD-" -description: null -organism: null -fragment: null }
Length of the longuest sequence
426
Number of gaps
1878
Do the sequences have the same length ?
true
Char at res 10 (10th sequence)
"E"
Substring between two residues in a sequence
"EP-PLSQETFSDLWKLLPENNVLSPLPS-QA-VDDLMLSPDDLAQWLTEDPGPDEAP---RMSEAAPHMAPTPAA-------PTPAAPAPAPSWPLSSSVPSQKTYHGSYGFRLGFLHSGTAKSVTCTYSPDLNKMFCQLAKTCPVQLWVDSTPPPGSRVRAMAIYKQSQHMTEVVRRCPHHERCSD-SDGLAPPQHLIRVEGNLRVEYSDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENFRKKGEPCHELP---PGSTKRALPN--NTS--SSPQ-PK-----KKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPAGSRAHSSHL-----KSKKGQSTSRHKKFMFKTEGPDSD-"
Converts a column number to a residue number in a sequence
47
Converts a residue number to a column number in a sequence
50
Creates a new alignment set from index 5 to 10
Amelaye\BioPHP\Domain\Sequence\Service\SequenceAlignmentManager {#419 -sequenceManager: Amelaye\BioPHP\Domain\Sequence\Builder\SequenceBuilder {#420 -sequence: Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#659 -primAcc: "sp|P04637|P53_HUMAN" -entryName: null -seqLength: 426 -start: 0 -end: 425 -molType: null -date: null -source: null -sequence: "MEEPQSDPSVEP-PLSQETFSDLWKLLPENNVLSPLPS-QA-MDDLMLSPDDIEQWFTEDPGPDEAP---RMPEAAPPVAPAPAA-------PTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSD-SDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELP---PGSTKRALPN--NTS--SSPQ-PK-----KKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPGGSRAHSSHL-----KSKKGQSTSRHKKLMFKTEGPDSD-" -description: null -organism: null -fragment: null } -sequenceManager: Amelaye\BioPHP\Domain\Sequence\Service\SequenceManager {#421 -elements: null -aminoApi: Amelaye\BioPHP\Api\AminoApi {#422 #bioapiClient: GuzzleHttp\Client {#432 -config: array:9 [ "base_uri" => GuzzleHttp\Psr7\Uri {#433 -scheme: "http" -userInfo: "" -host: "api.amelayes-biophp.net" -port: null -path: "" -query: "" -fragment: "" } "handler" => GuzzleHttp\HandlerStack {#423 -handler: GuzzleHttp\Handler\StreamHandler {#424 -lastHeaders: [] } -stack: array:6 [ 0 => array:2 [ 0 => Closure(callable $handler) {#425 : "GuzzleHttp\Middleware" } 1 => "http_errors" ] 1 => array:2 [ 0 => Closure(callable $handler) {#426 : "GuzzleHttp\Middleware" } 1 => "allow_redirects" ] 2 => array:2 [ 0 => Closure(callable $handler) {#427 : "GuzzleHttp\Middleware" } 1 => "cookies" ] 3 => array:2 [ 0 => Closure(callable $handler) {#428 : "GuzzleHttp\Middleware" } 1 => "prepare_body" ] 4 => array:2 [ 0 => Csa\GuzzleHttp\Middleware\Stopwatch\StopwatchMiddleware {#429 -stopwatch: Symfony\Component\Stopwatch\Stopwatch {#137 -morePrecision: true -sections: array:1 [ "__root__" => Symfony\Component\Stopwatch\Section {#136 -events: array:1 [ "__section__.child" => Symfony\Component\Stopwatch\StopwatchEvent {#153 -periods: [] -origin: 1594834443313.9 -category: "section" -morePrecision: true -started: array:1 [ 0 => -0.0 ] } ] -origin: null -morePrecision: true -id: null -children: array:1 [ 0 => Symfony\Component\Stopwatch\Section {#154 -events: array:36 [ "__section__" => Symfony\Component\Stopwatch\StopwatchEvent {#155 -periods: [] -origin: 1594834443313.9 -category: "default" -morePrecision: true -started: array:1 [ 0 => -0.0 ] } "kernel.request" => Symfony\Component\Stopwatch\StopwatchEvent {#156 -periods: array:1 [ 0 => Symfony\Component\Stopwatch\StopwatchPeriod {#197 -start: -0.0 -end: 6.1 -memory: 2097152 } ] -origin: 1594834443313.9 -category: "section" -morePrecision: true -started: [] } "Symfony\Component\HttpKernel\EventListener\DebugHandlersListener" => Symfony\Component\Stopwatch\StopwatchEvent {#157 -periods: array:1 [ 0 => Symfony\Component\Stopwatch\StopwatchPeriod {#159 -start: 0.1 -end: 0.3 -memory: 2097152 } ] -origin: 1594834443313.9 -category: "event_listener" -morePrecision: true -started: [] } "Symfony\Component\HttpKernel\EventListener\ValidateRequestListener" => Symfony\Component\Stopwatch\StopwatchEvent {#160 -periods: array:1 [ 0 => Symfony\Component\Stopwatch\StopwatchPeriod {#161 -start: 0.3 -end: 0.4 -memory: 2097152 } ] -origin: 1594834443313.9 -category: "event_listener" -morePrecision: true -started: [] } "Symfony\Component\HttpKernel\EventListener\TestSessionListener" => Symfony\Component\Stopwatch\StopwatchEvent {#162 -periods: array:1 [ 0 => Symfony\Component\Stopwatch\StopwatchPeriod {#170 -start: 0.4 -end: 1.2 -memory: 2097152 } ] -origin: 1594834443313.9 -category: "event_listener" -morePrecision: true -started: [] } "Symfony\Component\HttpKernel\EventListener\SessionListener" => Symfony\Component\Stopwatch\StopwatchEvent {#171 -periods: array:1 [ 0 => Symfony\Component\Stopwatch\StopwatchPeriod {#173 -start: 1.2 -end: 1.3 -memory: 2097152 } ] -origin: 1594834443313.9 -category: "event_listener" -morePrecision: true -started: [] } "Symfony\Component\HttpKernel\EventListener\LocaleListener" => Symfony\Component\Stopwatch\StopwatchEvent {#174 -periods: array:2 [ 0 => Symfony\Component\Stopwatch\StopwatchPeriod {#175 -start: 1.3 -end: 1.3 -memory: 2097152 } 1 => Symfony\Component\Stopwatch\StopwatchPeriod {#187 -start: 4.0 -end: 4.0 -memory: 2097152 } ] -origin: 1594834443313.9 -category: "event_listener" -morePrecision: true -started: [] } "Symfony\Component\HttpKernel\EventListener\RouterListener" => Symfony\Component\Stopwatch\StopwatchEvent {#176 -periods: array:1 [ 0 => Symfony\Component\Stopwatch\StopwatchPeriod {#190 -start: 1.3 -end: 3.9 -memory: 2097152 } ] -origin: 1594834443313.9 -category: "event_listener" -morePrecision: true -started: [] } "Symfony\Bundle\FrameworkBundle\EventListener\ResolveControllerNameSubscriber" => Symfony\Component\Stopwatch\StopwatchEvent {#189 -periods: array:1 [ 0 => Symfony\Component\Stopwatch\StopwatchPeriod {#188 -start: 4.0 -end: 4.0 -memory: 2097152 } ] -origin: 1594834443313.9 -category: "event_listener" -morePrecision: true -started: [] } "Symfony\Component\HttpKernel\EventListener\LocaleAwareListener" => Symfony\Component\Stopwatch\StopwatchEvent {#186 -periods: array:1 [ 0 => Symfony\Component\Stopwatch\StopwatchPeriod {#184 -start: 4.1 -end: 4.3 -memory: 2097152 } ] -origin: 1594834443313.9 -category: "event_listener" -morePrecision: true -started: [] } "Symfony\Bundle\SecurityBundle\Debug\TraceableFirewallListener" => Symfony\Component\Stopwatch\StopwatchEvent {#185 -periods: array:2 [ 0 => Symfony\Component\Stopwatch\StopwatchPeriod {#196 -start: 4.4 -end: 4.9 -memory: 2097152 } 1 => Symfony\Component\Stopwatch\StopwatchPeriod {#205 -start: 4.9 -end: 6.1 -memory: 2097152 } ] -origin: 1594834443313.9 -category: "event_listener" -morePrecision: true -started: [] } "controller.get_callable" => Symfony\Component\Stopwatch\StopwatchEvent {#206 -periods: array:1 [ 0 => Symfony\Component\Stopwatch\StopwatchPeriod {#198 -start: 6.9 -end: 7.1 -memory: 2097152 } ] -origin: 1594834443313.9 -category: "default" -morePrecision: true -started: [] } "kernel.controller" => Symfony\Component\Stopwatch\StopwatchEvent {#320 -periods: array:1 [ 0 => Symfony\Component\Stopwatch\StopwatchPeriod {#388 -start: 9.7 -end: 15.6 -memory: 2097152 } ] -origin: 1594834443313.9 -category: "section" -morePrecision: true -started: [] } "Symfony\Bundle\FrameworkBundle\DataCollector\RouterDataCollector" => Symfony\Component\Stopwatch\StopwatchEvent {#321 -periods: array:1 [ 0 => Symfony\Component\Stopwatch\StopwatchPeriod {#322 -start: 9.7 -end: 9.7 -memory: 2097152 } ] -origin: 1594834443313.9 -category: "event_listener" -morePrecision: true -started: [] } "Symfony\Component\HttpKernel\DataCollector\RequestDataCollector" => Symfony\Component\Stopwatch\StopwatchEvent {#323 -periods: array:1 [ 0 => Symfony\Component\Stopwatch\StopwatchPeriod {#324 -start: 9.7 -end: 9.8 -memory: 2097152 } ] -origin: 1594834443313.9 -category: "event_listener" -morePrecision: true -started: [] } "Sensio\Bundle\FrameworkExtraBundle\EventListener\ControllerListener" => Symfony\Component\Stopwatch\StopwatchEvent {#325 -periods: array:1 [ 0 => Symfony\Component\Stopwatch\StopwatchPeriod {#327 -start: 9.8 -end: 11.1 -memory: 2097152 } ] -origin: 1594834443313.9 -category: "event_listener" -morePrecision: true -started: [] } "Sensio\Bundle\FrameworkExtraBundle\EventListener\ParamConverterListener" => Symfony\Component\Stopwatch\StopwatchEvent {#326 -periods: array:1 [ 0 => Symfony\Component\Stopwatch\StopwatchPeriod {#331 -start: 11.1 -end: 15.5 -memory: 2097152 } ] -origin: 1594834443313.9 -category: "event_listener" -morePrecision: true -started: [] } "Sensio\Bundle\FrameworkExtraBundle\EventListener\HttpCacheListener" => Symfony\Component\Stopwatch\StopwatchEvent {#336 -periods: array:1 [ 0 => Symfony\Component\Stopwatch\StopwatchPeriod {#335 -start: 15.5 -end: 15.6 -memory: 2097152 } ] -origin: 1594834443313.9 -category: "event_listener" -morePrecision: true -started: [] } "Sensio\Bundle\FrameworkExtraBundle\EventListener\TemplateListener" => Symfony\Component\Stopwatch\StopwatchEvent {#386 -periods: array:1 [ 0 => Symfony\Component\Stopwatch\StopwatchPeriod {#387 -start: 15.6 -end: 15.6 -memory: 2097152 } ] -origin: 1594834443313.9 -category: "event_listener" -morePrecision: true -started: [] } "controller.get_arguments" => Symfony\Component\Stopwatch\StopwatchEvent {#389 -periods: array:1 [ 0 => Symfony\Component\Stopwatch\StopwatchPeriod {#415 -start: 16.0 -end: 673.1 -memory: 2097152 } ] -origin: 1594834443313.9 -category: "default" -morePrecision: true -started: [] } "Symfony\Component\HttpKernel\Controller\ArgumentResolver\RequestAttributeValueResolver::supports" => Symfony\Component\Stopwatch\StopwatchEvent {#395 -periods: array:1 [ 0 => Symfony\Component\Stopwatch\StopwatchPeriod {#396 -start: 16.3 -end: 16.3 -memory: 2097152 } ] -origin: 1594834443313.9 -category: "controller.argument_value_resolver" -morePrecision: true -started: [] } "Symfony\Component\HttpKernel\Controller\ArgumentResolver\RequestValueResolver::supports" => Symfony\Component\Stopwatch\StopwatchEvent {#399 -periods: array:1 [ 0 => Symfony\Component\Stopwatch\StopwatchPeriod {#400 -start: 16.4 -end: 16.4 -memory: 2097152 } ] -origin: 1594834443313.9 -category: "controller.argument_value_resolver" -morePrecision: true -started: [] } "Symfony\Component\HttpKernel\Controller\ArgumentResolver\SessionValueResolver::supports" => Symfony\Component\Stopwatch\StopwatchEvent {#403 -periods: array:1 [ 0 => Symfony\Component\Stopwatch\StopwatchPeriod {#404 -start: 16.4 -end: 16.4 -memory: 2097152 } ] -origin: 1594834443313.9 -category: "controller.argument_value_resolver" -morePrecision: true -started: [] } "Symfony\Component\Security\Http\Controller\UserValueResolver::supports" => Symfony\Component\Stopwatch\StopwatchEvent {#407 -periods: array:1 [ 0 => Symfony\Component\Stopwatch\StopwatchPeriod {#408 -start: 16.5 -end: 16.5 -memory: 2097152 } ] -origin: 1594834443313.9 -category: "controller.argument_value_resolver" -morePrecision: true -started: [] } "Symfony\Component\HttpKernel\Controller\ArgumentResolver\ServiceValueResolver::supports" => Symfony\Component\Stopwatch\StopwatchEvent {#412 -periods: array:1 [ 0 => Symfony\Component\Stopwatch\StopwatchPeriod {#414 -start: 16.6 -end: 16.6 -memory: 2097152 } ] -origin: 1594834443313.9 -category: "controller.argument_value_resolver" -morePrecision: true -started: [] } "Symfony\Component\HttpKernel\Controller\ArgumentResolver\ServiceValueResolver::resolve" => Symfony\Component\Stopwatch\StopwatchEvent {#417 -periods: array:1 [ 0 => Symfony\Component\Stopwatch\StopwatchPeriod {#418 -start: 16.6 -end: 673.1 -memory: 2097152 } ] -origin: 1594834443313.9 -category: "controller.argument_value_resolver" -morePrecision: true -started: [] } "GET http://api.amelayes-biophp.net/aminos" => Symfony\Component\Stopwatch\StopwatchEvent {#514 -periods: array:1 [ 0 => Symfony\Component\Stopwatch\StopwatchPeriod {#523 -start: 21.1 -end: 487.5 -memory: 2097152 } ] -origin: 1594834443313.9 -category: "default" -morePrecision: true -started: [] } "GET http://api.amelayes-biophp.net/nucleotids" => Symfony\Component\Stopwatch\StopwatchEvent {#566 -periods: array:1 [ 0 => Symfony\Component\Stopwatch\StopwatchPeriod {#575 -start: 490.4 -end: 589.4 -memory: 2097152 } ] -origin: 1594834443313.9 -category: "default" -morePrecision: true -started: [] } "GET http://api.amelayes-biophp.net/elements/6" => Symfony\Component\Stopwatch\StopwatchEvent {#589 -periods: array:1 [ 0 => Symfony\Component\Stopwatch\StopwatchPeriod {#598 -start: 590.6 -end: 671.3 -memory: 2097152 } ] -origin: 1594834443313.9 -category: "default" -morePrecision: true -started: [] } "kernel.controller_arguments" => Symfony\Component\Stopwatch\StopwatchEvent {#617 -periods: 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"Doctrine\ORM\PersistentCollection" ] 3 => array:4 [ 0 => array:2 [ 0 => "jms_serializer.doctrine_proxy_subscriber" 1 => "onPreSerialize" ] 1 => null 2 => null 3 => "Doctrine\ODM\MongoDB\PersistentCollection" ] 4 => array:4 [ 0 => array:2 [ 0 => "jms_serializer.doctrine_proxy_subscriber" 1 => "onPreSerialize" ] 1 => null 2 => null 3 => "Doctrine\ODM\PHPCR\PersistentCollection" ] 5 => array:4 [ 0 => array:2 [ 0 => "jms_serializer.doctrine_proxy_subscriber" 1 => "onPreSerialize" ] 1 => null 2 => null 3 => "Doctrine\Common\Persistence\Proxy" ] 6 => array:4 [ 0 => array:2 [ 0 => "jms_serializer.doctrine_proxy_subscriber" 1 => "onPreSerialize" ] 1 => null 2 => null 3 => "ProxyManager\Proxy\LazyLoadingInterface" ] ] "serializer.post_serialize" => array:1 [ 0 => array:4 [ 0 => array:2 [ 0 => "jms_serializer.stopwatch_subscriber" 1 => "onPostSerialize" ] 1 => null 2 => null 3 => null ] ] ] -classListeners: [] } -expressionEvaluator: JMS\Serializer\Expression\ExpressionEvaluator {#443} } 1 => JMS\Serializer\GraphNavigator\Factory\SerializationGraphNavigatorFactory {#450 -metadataFactory: Metadata\MetadataFactory {#435} -handlerRegistry: JMS\Serializer\Handler\LazyHandlerRegistry {#439} -accessor: JMS\Serializer\Accessor\DefaultAccessorStrategy {#442} -dispatcher: JMS\Serializer\EventDispatcher\LazyEventDispatcher {#456} -expressionEvaluator: JMS\Serializer\Expression\ExpressionEvaluator {#443} } ] } #apiKey: null } -nucleotidApi: Amelaye\BioPHP\Api\NucleotidApi {#502 #bioapiClient: GuzzleHttp\Client {#432} #serializer: JMS\Serializer\Serializer {#434} #apiKey: null } -nucleotids: array:8 [ 0 => Amelaye\BioPHP\Api\DTO\NucleotidDTO {#532 -id: null -letter: "A" -complement: "T" -nature: "DNA" -weight: 313.245 } 1 => Amelaye\BioPHP\Api\DTO\NucleotidDTO {#525 -id: null -letter: "T" -complement: "A" -nature: "DNA" -weight: 304.225 } 2 => Amelaye\BioPHP\Api\DTO\NucleotidDTO {#581 -id: null -letter: "G" -complement: "C" -nature: "DNA" -weight: 329.245 } 3 => Amelaye\BioPHP\Api\DTO\NucleotidDTO {#582 -id: null -letter: "C" -complement: "G" -nature: "DNA" -weight: 289.215 } 4 => Amelaye\BioPHP\Api\DTO\NucleotidDTO {#583 -id: null -letter: "A" -complement: "U" -nature: "RNA" -weight: 329.245 } 5 => Amelaye\BioPHP\Api\DTO\NucleotidDTO {#584 -id: null -letter: "U" -complement: "A" -nature: "RNA" -weight: 306.195 } 6 => Amelaye\BioPHP\Api\DTO\NucleotidDTO {#585 -id: null -letter: "G" -complement: "C" -nature: "RNA" -weight: 345.245 } 7 => Amelaye\BioPHP\Api\DTO\NucleotidDTO {#586 -id: null -letter: "C" -complement: "G" -nature: "RNA" -weight: 305.215 } ] -water: Amelaye\BioPHP\Api\DTO\ElementDTO {#609 -id: 6 -name: "water" -weight: 18.015 } -aminos: array:26 [ 0 => Amelaye\BioPHP\Api\DTO\AminoDTO {#530 -id: "*" -name: "STOP" -name1Letter: "*" -name3Letters: "STP" -weight1: 0.0 -weight2: 0.0 -residueMolWeight: 0.0 } 1 => Amelaye\BioPHP\Api\DTO\AminoDTO {#539 -id: "A" -name: "Alanine" -name1Letter: "A" -name3Letters: "Ala" -weight1: 89.09 -weight2: 89.09 -residueMolWeight: 71.07 } 2 => Amelaye\BioPHP\Api\DTO\AminoDTO {#540 -id: "B" -name: "Aspartate or asparagine" -name1Letter: "B" -name3Letters: "N/A" -weight1: 132.12 -weight2: 132.1 -residueMolWeight: 0.0 } 3 => Amelaye\BioPHP\Api\DTO\AminoDTO {#541 -id: "C" -name: "Cysteine" -name1Letter: "C" -name3Letters: "Cys" -weight1: 121.15 -weight2: 121.15 -residueMolWeight: 103.1 } 4 => Amelaye\BioPHP\Api\DTO\AminoDTO {#542 -id: "D" -name: "Aspartic acid" -name1Letter: "D" -name3Letters: "Asp" -weight1: 133.1 -weight2: 133.1 -residueMolWeight: 115.08 } 5 => Amelaye\BioPHP\Api\DTO\AminoDTO {#543 -id: "E" -name: "Glutamic acid" -name1Letter: "E" -name3Letters: "Glu" -weight1: 147.13 -weight2: 147.13 -residueMolWeight: 129.11 } 6 => Amelaye\BioPHP\Api\DTO\AminoDTO {#544 -id: "F" -name: "Phenylalanine" -name1Letter: "F" -name3Letters: "Phe" -weight1: 165.19 -weight2: 165.19 -residueMolWeight: 147.17 } 7 => Amelaye\BioPHP\Api\DTO\AminoDTO {#545 -id: "G" -name: "Glycine" -name1Letter: "G" -name3Letters: "Gly" -weight1: 75.07 -weight2: 75.07 -residueMolWeight: 57.05 } 8 => Amelaye\BioPHP\Api\DTO\AminoDTO {#546 -id: "H" -name: "Histidine" -name1Letter: "H" -name3Letters: "His" -weight1: 155.16 -weight2: 155.16 -residueMolWeight: 137.14 } 9 => Amelaye\BioPHP\Api\DTO\AminoDTO {#547 -id: "I" -name: "Isoleucine" -name1Letter: "I" -name3Letters: "Ile" -weight1: 131.18 -weight2: 131.18 -residueMolWeight: 113.15 } 10 => Amelaye\BioPHP\Api\DTO\AminoDTO {#548 -id: "K" -name: "Lysine" -name1Letter: "K" -name3Letters: "Lys" -weight1: 146.19 -weight2: 146.19 -residueMolWeight: 128.17 } 11 => Amelaye\BioPHP\Api\DTO\AminoDTO {#549 -id: "L" -name: "Leucine" -name1Letter: "L" -name3Letters: "Leu" -weight1: 131.18 -weight2: 131.18 -residueMolWeight: 113.15 } 12 => Amelaye\BioPHP\Api\DTO\AminoDTO {#550 -id: "M" -name: "Methionine" -name1Letter: "M" -name3Letters: "Met" -weight1: 149.22 -weight2: 149.22 -residueMolWeight: 131.19 } 13 => Amelaye\BioPHP\Api\DTO\AminoDTO {#551 -id: "N" -name: "Asparagine" -name1Letter: "N" -name3Letters: "Asn" -weight1: 132.12 -weight2: 132.12 -residueMolWeight: 114.08 } 14 => Amelaye\BioPHP\Api\DTO\AminoDTO {#552 -id: "O" -name: "Pyrrolysine" -name1Letter: "O" -name3Letters: "Pyr" -weight1: 255.31 -weight2: 255.31 -residueMolWeight: 0.0 } 15 => Amelaye\BioPHP\Api\DTO\AminoDTO {#553 -id: "P" -name: "Proline" -name1Letter: "P" -name3Letters: "Pro" -weight1: 115.13 -weight2: 115.13 -residueMolWeight: 97.11 } 16 => Amelaye\BioPHP\Api\DTO\AminoDTO {#554 -id: "Q" -name: "Glutamine" -name1Letter: "Q" -name3Letters: "Gin" -weight1: 146.15 -weight2: 146.15 -residueMolWeight: 128.13 } 17 => Amelaye\BioPHP\Api\DTO\AminoDTO {#555 -id: "R" -name: "Arginine" -name1Letter: "R" -name3Letters: "Arg" -weight1: 174.21 -weight2: 174.21 -residueMolWeight: 156.18 } 18 => Amelaye\BioPHP\Api\DTO\AminoDTO {#556 -id: "S" -name: "Serine" -name1Letter: "S" -name3Letters: "Ser" -weight1: 105.09 -weight2: 105.09 -residueMolWeight: 87.07 } 19 => Amelaye\BioPHP\Api\DTO\AminoDTO {#557 -id: "T" -name: "Threonine" -name1Letter: "T" -name3Letters: "Thr" -weight1: 119.12 -weight2: 119.12 -residueMolWeight: 101.1 } 20 => Amelaye\BioPHP\Api\DTO\AminoDTO {#558 -id: "U" -name: "Selenocysteine" -name1Letter: "U" -name3Letters: "Sec" -weight1: 168.05 -weight2: 168.05 -residueMolWeight: 0.0 } 21 => Amelaye\BioPHP\Api\DTO\AminoDTO {#559 -id: "V" -name: "Valine" -name1Letter: "V" -name3Letters: "Val" -weight1: 117.15 -weight2: 117.15 -residueMolWeight: 99.13 } 22 => Amelaye\BioPHP\Api\DTO\AminoDTO {#560 -id: "W" -name: "Tryptophan" -name1Letter: "W" -name3Letters: "Trp" -weight1: 204.22 -weight2: 204.22 -residueMolWeight: 186.2 } 23 => Amelaye\BioPHP\Api\DTO\AminoDTO {#561 -id: "X" -name: "Any" -name1Letter: "X" -name3Letters: "XXX" -weight1: 75.07 -weight2: 204.22 -residueMolWeight: 114.82 } 24 => Amelaye\BioPHP\Api\DTO\AminoDTO {#562 -id: "Y" -name: "Tyrosine" -name1Letter: "Y" -name3Letters: "Tyr" -weight1: 181.19 -weight2: 181.19 -residueMolWeight: 163.17 } 25 => Amelaye\BioPHP\Api\DTO\AminoDTO {#563 -id: "Z" -name: "Glutamate or glutamine" -name1Letter: "Z" -name3Letters: "N/A" -weight1: 146.15 -weight2: 147.13 -residueMolWeight: 0.0 } ] } } -aAlphabet: array:26 [ 0 => "A" 1 => "B" 2 => "C" 3 => "D" 4 => "E" 5 => "F" 6 => "G" 7 => "H" 8 => "I" 9 => "J" 10 => "K" 11 => "L" 12 => "M" 13 => "N" 14 => "O" 15 => "P" 16 => "Q" 17 => "R" 18 => "S" 19 => "T" 20 => "U" 21 => "V" 22 => "W" 23 => "X" 24 => "Y" 25 => "Z" ] -iLength: 426 -iGapCount: 166 -aSeqSet: ArrayIterator {#681 : false : false : array:3 [ 0 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#677 -primAcc: "sp|P07193|P53_XENLA" -entryName: null -seqLength: 426 -start: 0 -end: 425 -molType: null -date: null -source: null -sequence: "-MEPSSETGMDP-PLSQETFEDLWSLLPDPLQTVTCR------------LDNLSEFPDY------PL-AADMT-----------V-------LQEGLMGNAVPTVTSCAVPSTDDYAGKYGLQLDFQQNGTAKSVTCTYSPELNKLFCQLAKTCPLLVRVESPPPRGSILRATAVYKKSEHVAEVVKRCPHHERSVEPGEDAAPPSHLMRVEGNLQAYYMEDVNSGRHSVCVPYEGPQVGTECTTVLYNYMCNSSCMGGMNRRPILTIITLETPQGLLLGRRCFEVRVCACPGRDRRTEEDNYTKKRGLKPSG--------KRELAH--PPS--SEPPLPK-KRLVVVDDDEEIFTLRIKGRSRYEMIKKLNDALELQESLDQQK--------VTIKCR--KCRDEIKPKKGKKLLVKDEQPDSE-" -description: null -organism: null -fragment: null } 1 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#650 -primAcc: "sp|P10360|P53_CHICK" -entryName: null -seqLength: 426 -start: 0 -end: 425 -molType: null -date: null -source: null -sequence: "MAE-----EMEPLLEPTEVFMDLWSMLPY-------------SMQQLPLPEDHSNWQELSPLEPSDP---PPPPPPPPLPLAAAA-------PPPLNPPTPPRAAPSPVVPSTEDYGGDFDFRVGFVEAGTAKSVTCTYSPVLNKVYCRLAKPCPVQVRVGVAPPPGSSLRAVAVYKKSEHVAEVVRRCPHHERCGGGTDGLAPAQHLIRVEGNPQARYHDDETTKRHSVVVPYEPPEVGSDCTTVLYNFMCNSSCMGGMNRRPILTILTLEGPGGQLLGRRCFEVRVCACPGRDRKIEEENFRKRGGAG--------GVAKRAMSP--PTEA-PEPPKKR-----VLNPDNEIFYLQVRGRRRYEMLKEINEALQLAEGGSAPRPSKGRR----------VKVEGPQPSCGKKLLQKGSD-----" -description: null -organism: null -fragment: null } 2 => Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#673 -primAcc: "sp|P51664|P53_SHEEP" -entryName: null -seqLength: 426 -start: 0 -end: 425 -molType: null -date: null -source: null -sequence: "MEESQAELGVEP-PLSQETFSDLWNLLPENNLLSSELS-AP-VDDLLPYSEDVVTWLDE--CPNEAP---QMPEPPAQA-----------------ALAPATSWPLSSFVPSQKTYPGNYGFRLGFLHSGTAKSVTCTYSPSLNKLFCQLAKTCPVQLWVDSPPPPGTRVRAMAIYKKLEHMTEVVRRSPHHERSSDYSDGLAPPQHLIRVEGNLRAEYFDDRNTFRHSVVVPYESPEIESECTTIHYNFMCNSSCMGGMNRRPILTIITLEDSRGNLLGRSSFEVRVCACPGRDRRTEEENFRKKGQSCPEPP---PGSTKRALPS--STS--SSPQ-QK-----KKPLDGEYFTLQIRGRKRFEMFRELNEALELMDAQAGREPGESRAHSSHL-----KSKKGPSPSCHKKPMLKREGPDSD-" -description: null -organism: null -fragment: null } ] } -bFlush: true -sFilename: "data/clustal.txt" -sFormat: "CLUSTAL" }
Creates a new alignment with selected indexes
Amelaye\BioPHP\Domain\Sequence\Service\SequenceAlignmentManager {#419 -sequenceManager: Amelaye\BioPHP\Domain\Sequence\Builder\SequenceBuilder {#420 -sequence: Amelaye\BioPHP\Domain\Sequence\Entity\Sequence {#659 -primAcc: "sp|P04637|P53_HUMAN" -entryName: null -seqLength: 426 -start: 0 -end: 425 -molType: null -date: null -source: null -sequence: "MEEPQSDPSVEP-PLSQETFSDLWKLLPENNVLSPLPS-QA-MDDLMLSPDDIEQWFTEDPGPDEAP---RMPEAAPPVAPAPAA-------PTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSD-SDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELP---PGSTKRALPN--NTS--SSPQ-PK-----KKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPGGSRAHSSHL-----KSKKGQSTSRHKKLMFKTEGPDSD-" -description: null -organism: null -fragment: null } -sequenceManager: Amelaye\BioPHP\Domain\Sequence\Service\SequenceManager {#421 -elements: null -aminoApi: Amelaye\BioPHP\Api\AminoApi {#422 #bioapiClient: 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#_regex: null #_ast: null #_value: null #_kept: true #_unification: -1 #_name: 10 #_children: null #_nodeId: null #_nodeOptions: [] #_defaultId: null #_defaultOptions: [] #_pp: null #_transitional: true } 11 => Hoa\Compiler\Llk\Rule\Token {#478 #_tokenName: "_quote" #_namespace: null #_regex: null #_ast: null #_value: null #_kept: false #_unification: -1 #_name: 11 #_children: null #_nodeId: null #_nodeOptions: [] #_defaultId: null #_defaultOptions: [] #_pp: null #_transitional: true } 12 => Hoa\Compiler\Llk\Rule\Concatenation {#479 #_name: 12 #_children: array:3 [ 0 => 9 1 => 10 2 => 11 ] #_nodeId: "#simple_type" #_nodeOptions: [] #_defaultId: null #_defaultOptions: [] #_pp: null #_transitional: true } 13 => Hoa\Compiler\Llk\Rule\Token {#480 #_tokenName: "apostrophe_" #_namespace: null #_regex: null #_ast: null #_value: null #_kept: false #_unification: -1 #_name: 13 #_children: null #_nodeId: null #_nodeOptions: [] #_defaultId: null #_defaultOptions: [] #_pp: null #_transitional: true } 14 => Hoa\Compiler\Llk\Rule\Token {#481 #_tokenName: "apostrophed_string" #_namespace: null #_regex: null #_ast: null #_value: null #_kept: true #_unification: -1 #_name: 14 #_children: null #_nodeId: null #_nodeOptions: [] #_defaultId: null #_defaultOptions: [] #_pp: null #_transitional: true } 15 => Hoa\Compiler\Llk\Rule\Token {#482 #_tokenName: "_apostrophe" #_namespace: null #_regex: null #_ast: null #_value: null #_kept: false #_unification: -1 #_name: 15 #_children: null #_nodeId: null #_nodeOptions: [] #_defaultId: null #_defaultOptions: [] #_pp: null #_transitional: true } 16 => Hoa\Compiler\Llk\Rule\Concatenation {#483 #_name: 16 #_children: array:3 [ 0 => 13 1 => 14 2 => 15 ] #_nodeId: "#simple_type" #_nodeOptions: [] #_defaultId: null #_defaultOptions: [] #_pp: null #_transitional: true } 17 => Hoa\Compiler\Llk\Rule\Concatenation {#484 #_name: 17 #_children: array:1 [ 0 => "array" ] #_nodeId: "#simple_type" #_nodeOptions: [] #_defaultId: null #_defaultOptions: [] #_pp: null #_transitional: true } "simple_type" => Hoa\Compiler\Llk\Rule\Choice {#485 #_name: "simple_type" #_children: array:7 [ 0 => 2 1 => 4 2 => 6 3 => 8 4 => 12 5 => 16 6 => 17 ] #_nodeId: null #_nodeOptions: [] #_defaultId: "#simple_type" #_defaultOptions: [] #_pp: " <name> | <number> | <null> | <empty_string> | ::quote_:: <quoted_string> ::_quote:: | ::apostrophe_:: <apostrophed_string> ::_apostrophe:: | array()" #_transitional: false } 19 => Hoa\Compiler\Llk\Rule\Token {#486 #_tokenName: "name" #_namespace: null #_regex: null #_ast: null #_value: null #_kept: true #_unification: -1 #_name: 19 #_children: null #_nodeId: null #_nodeOptions: [] #_defaultId: null #_defaultOptions: [] #_pp: null #_transitional: true } 20 => Hoa\Compiler\Llk\Rule\Token {#487 #_tokenName: "parenthesis_" #_namespace: null #_regex: null #_ast: null #_value: null #_kept: false #_unification: -1 #_name: 20 #_children: null #_nodeId: null #_nodeOptions: [] #_defaultId: null #_defaultOptions: [] #_pp: null #_transitional: true } 21 => Hoa\Compiler\Llk\Rule\Token {#488 #_tokenName: "comma" #_namespace: null #_regex: null #_ast: null #_value: null #_kept: false #_unification: -1 #_name: 21 #_children: null #_nodeId: null #_nodeOptions: [] #_defaultId: null #_defaultOptions: [] #_pp: null #_transitional: true } 22 => Hoa\Compiler\Llk\Rule\Concatenation {#489 #_name: 22 #_children: array:2 [ 0 => 21 1 => "type" ] #_nodeId: "#compound_type" #_nodeOptions: [] #_defaultId: null #_defaultOptions: [] #_pp: null #_transitional: true } 23 => Hoa\Compiler\Llk\Rule\Repetition {#490 #_min: 0 #_max: -1 #_name: 23 #_children: 22 #_nodeId: null #_nodeOptions: [] #_defaultId: null #_defaultOptions: [] #_pp: null #_transitional: true } 24 => Hoa\Compiler\Llk\Rule\Token {#491 #_tokenName: "_parenthesis" #_namespace: null #_regex: null #_ast: null #_value: null #_kept: false #_unification: -1 #_name: 24 #_children: null #_nodeId: null #_nodeOptions: [] #_defaultId: null #_defaultOptions: [] #_pp: null #_transitional: true } "compound_type" => Hoa\Compiler\Llk\Rule\Concatenation {#492 #_name: "compound_type" #_children: array:5 [ 0 => 19 1 => 20 2 => "type" 3 => 23 4 => 24 ] #_nodeId: null #_nodeOptions: [] #_defaultId: "#compound_type" #_defaultOptions: [] #_pp: " <name> ::parenthesis_:: type() ( ::comma:: type() )* ::_parenthesis::" #_transitional: false } 26 => Hoa\Compiler\Llk\Rule\Token {#493 #_tokenName: "array_" #_namespace: null #_regex: null #_ast: null #_value: null #_kept: false #_unification: -1 #_name: 26 #_children: null #_nodeId: null #_nodeOptions: [] #_defaultId: null #_defaultOptions: [] #_pp: null #_transitional: true } 27 => Hoa\Compiler\Llk\Rule\Token {#494 #_tokenName: "comma" #_namespace: null #_regex: null #_ast: null #_value: null #_kept: false #_unification: -1 #_name: 27 #_children: null #_nodeId: null #_nodeOptions: [] #_defaultId: null #_defaultOptions: [] #_pp: null #_transitional: true } 28 => Hoa\Compiler\Llk\Rule\Concatenation {#495 #_name: 28 #_children: array:2 [ 0 => 27 1 => "simple_type" ] #_nodeId: "#array" #_nodeOptions: [] #_defaultId: null #_defaultOptions: [] #_pp: null #_transitional: true } 29 => Hoa\Compiler\Llk\Rule\Repetition {#496 #_min: 0 #_max: -1 #_name: 29 #_children: 28 #_nodeId: null #_nodeOptions: [] #_defaultId: null #_defaultOptions: [] #_pp: null #_transitional: true } 30 => Hoa\Compiler\Llk\Rule\Concatenation {#497 #_name: 30 #_children: array:2 [ 0 => "simple_type" 1 => 29 ] #_nodeId: null #_nodeOptions: [] #_defaultId: null #_defaultOptions: [] #_pp: null #_transitional: true } 31 => Hoa\Compiler\Llk\Rule\Repetition {#498 #_min: 0 #_max: 1 #_name: 31 #_children: 30 #_nodeId: null #_nodeOptions: [] #_defaultId: null #_defaultOptions: [] #_pp: null #_transitional: true } 32 => Hoa\Compiler\Llk\Rule\Token {#499 #_tokenName: "_array" #_namespace: null #_regex: null #_ast: null #_value: null #_kept: false #_unification: -1 #_name: 32 #_children: null #_nodeId: null #_nodeOptions: [] #_defaultId: null #_defaultOptions: [] #_pp: null #_transitional: true } "array" => Hoa\Compiler\Llk\Rule\Concatenation {#500 #_name: "array" #_children: array:3 [ 0 => 26 1 => 31 2 => 32 ] #_nodeId: null #_nodeOptions: [] #_defaultId: "#array" #_defaultOptions: [] #_pp: " ::array_:: ( simple_type() ( ::comma:: simple_type() )* )? ::_array::" #_transitional: false } ] #_tokenSequence: Hoa\Iterator\Buffer {#599 #_iterator: Generator {#596 : Hoa\Compiler\Llk\Lexer {#600 …} : { { Hoa\Compiler\Llk\Lexer->lexMe($text, array $tokens) … ›];›}› } } : false } #_buffer: SplDoublyLinkedList {#603 : IT_MODE_FIFO | IT_MODE_KEEP : array:2 [ 0 => array:2 [ 0 => 0 1 => array:6 [ "token" => "name" "value" => "Amelaye\BioPHP\Api\DTO\ElementDTO" "length" => 33 "namespace" => "default" "keep" => true "offset" => 0 ] ] 1 => array:2 [ 0 => 1 1 => array:6 [ "token" => "EOF" "value" => "EOF" "length" => 0 "namespace" => "default" "keep" => true "offset" => 33 ] ] ] } #_bufferSize: 1024 : Generator {#596} } #_errorToken: array:6 [ "token" => "EOF" "value" => "EOF" "length" => 0 "namespace" => "default" "keep" => true "offset" => 33 ] #_trace: array:7 [ 0 => Hoa\Compiler\Llk\Rule\Entry {#531 #_rule: "type" #_data: 0 #_todo: array:1 [ 0 => Hoa\Compiler\Llk\Rule\Ekzit {#529 #_rule: "type" #_data: 0 #_todo: null #_depth: 0 #_transitional: false } ] #_depth: 0 #_transitional: false } 1 => Hoa\Compiler\Llk\Rule\Entry {#534 #_rule: "simple_type" #_data: 0 #_todo: array:2 [ 0 => Hoa\Compiler\Llk\Rule\Ekzit {#529} 1 => Hoa\Compiler\Llk\Rule\Ekzit {#524 #_rule: "simple_type" #_data: 0 #_todo: null #_depth: 1 #_transitional: false } ] #_depth: 1 #_transitional: false } 2 => Hoa\Compiler\Llk\Rule\Entry {#533 #_rule: 2 #_data: 0 #_todo: null #_depth: 1 #_transitional: true } 3 => Hoa\Compiler\Llk\Rule\Token {#576 #_tokenName: "name" #_namespace: "default" #_regex: "(?:[a-zA-Z_\x7f-\xff][a-zA-Z0-9_\x7f-\xff]*\\)*[a-zA-Z_\x7f-\xff][a-zA-Z0-9_\x7f-\xff]*" #_ast: null #_value: "Amelaye\BioPHP\Api\DTO\ElementDTO" #_kept: true #_unification: -1 #_name: 1 #_children: null #_nodeId: null #_nodeOptions: [] #_defaultId: null #_defaultOptions: [] #_pp: null #_transitional: true } 4 => Hoa\Compiler\Llk\Rule\Ekzit {#535 #_rule: 2 #_data: 0 #_todo: null #_depth: 1 #_transitional: true } 5 => Hoa\Compiler\Llk\Rule\Ekzit {#524} 6 => Hoa\Compiler\Llk\Rule\Ekzit {#529} ] #_todo: [] #_tree: Hoa\Compiler\Llk\TreeNode {#580 #_id: "#simple_type" #_value: null #_children: array:1 [ 0 => Hoa\Compiler\Llk\TreeNode {#573 #_id: "token" #_value: array:3 [ "token" => "name" "value" => "Amelaye\BioPHP\Api\DTO\ElementDTO" "namespace" => "default" ] #_children: [] #_parent: Hoa\Compiler\Llk\TreeNode {#580} #_data: [] } ] #_parent: null #_data: [] } #_depth: -1 } -visitor: JMS\Serializer\Type\TypeVisitor {#501} } -serializationVisitors: array:2 [ "json" => JMS\Serializer\Visitor\Factory\JsonSerializationVisitorFactory {#459 -options: 1024 } "xml" => JMS\Serializer\Visitor\Factory\XmlSerializationVisitorFactory {#460 -defaultRootName: "result" -defaultVersion: "1.0" -defaultEncoding: "UTF-8" -formatOutput: true -defaultRootNamespace: null } ] -deserializationVisitors: array:2 [ "json" => JMS\Serializer\Visitor\Factory\JsonDeserializationVisitorFactory {#461 -options: 0 -depth: 512 } "xml" => JMS\Serializer\Visitor\Factory\XmlDeserializationVisitorFactory {#462 -disableExternalEntities: true -doctypeWhitelist: [] -options: 0 } ] -serializationContextFactory: JMS\SerializerBundle\ContextFactory\ConfiguredContextFactory {#463 -version: null -serializeNulls: null -enableMaxDepthChecks: false -attributes: [] -groups: [] } -deserializationContextFactory: JMS\SerializerBundle\ContextFactory\ConfiguredContextFactory {#464 -version: null -serializeNulls: null -enableMaxDepthChecks: false -attributes: [] -groups: [] } -graphNavigators: array:2 [ 2 => JMS\Serializer\GraphNavigator\Factory\DeserializationGraphNavigatorFactory {#438 -metadataFactory: Metadata\MetadataFactory {#435} -handlerRegistry: JMS\Serializer\Handler\LazyHandlerRegistry {#439 -container: Symfony\Component\DependencyInjection\Argument\ServiceLocator {#440 -factory: Symfony\Component\DependencyInjection\Container::getService($registry, string $id, ?string $method, $load) {#33 : Container4EQfUsr\srcApp_KernelTestDebugContainer {#32 …20} } -serviceMap: array:5 [ "jms_serializer.array_collection_handler" => array:4 [ 0 => "privates" 1 => "jms_serializer.array_collection_handler" 2 => "getJmsSerializer_ArrayCollectionHandlerService" 3 => false ] "jms_serializer.constraint_violation_handler" => array:4 [ 0 => "privates" 1 => "jms_serializer.constraint_violation_handler" 2 => "getJmsSerializer_ConstraintViolationHandlerService"