{"id":28454,"date":"2015-10-05T13:46:08","date_gmt":"2015-10-05T11:46:08","guid":{"rendered":"https:\/\/www.embl.org\/ells\/teachingbase\/opsins-bioinformatics\/part-2-multiple-sequence-alignment-of-protein-sequences\/"},"modified":"2021-06-18T15:03:36","modified_gmt":"2021-06-18T15:03:36","slug":"part-2-multiple-sequence-alignment-of-protein-sequences","status":"publish","type":"teachingbase","link":"https:\/\/www.embl.org\/ells\/teachingbase\/opsins-bioinformatics\/part-2-multiple-sequence-alignment-of-protein-sequences\/?lang=cs","title":{"rendered":"\u010c\u00e1st 2: Mnoho\u010detn\u00e1 p\u0159i\u0159azen\u00ed proteinov\u00fdch sekvenc\u00ed (multiple sequence alignment)"},"content":{"rendered":"\n<div class=\"wp-block-group\"><div class=\"wp-block-group__inner-container is-layout-flow wp-block-group-is-layout-flow\">\n<div class=\"vf-tabs\"><ul class=\"vf-tabs__list\" data-vf-js-tabs=\"true\"><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-53c12c03-fd69-4c60-a98c-517e493c9be7\">Overview<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-3ca77dbd-92bb-40c5-90ff-80bab24f0706\">Va\u0161e \u00faloha<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-fb7f8c0d-e668-4b4b-a403-3125a01d76f8\">Sekvence<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-49802ed2-ad8e-4020-8ef1-38a6e6070f30\">MUSCLE<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-f3293f44-6770-44b4-aa21-2e837496da09\">Ot\u00e1zky<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-52f5c833-db34-493c-919c-efbbcbcdb5cc\">Activity navigation<\/a><\/li><\/ul><div class=\"vf-tabs-content\" data-vf-js-tabs-content=\"true\">\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-53c12c03-fd69-4c60-a98c-517e493c9be7\"><h2>Overview<\/h2>\n<p>V\u00fdborn\u011b! V prvn\u00ed \u00faloze jste pravd\u011bpodobn\u011b zjistili, \u017ee n\u00e1\u0161 nezn\u00e1m\u00fd protein byl hov\u011bz\u00ed rhodopsin &#8211; sv\u011btlo\u010divn\u00e1 molekula v s\u00edtnici oka. Te\u010f se pokus\u00edme dozv\u011bd\u011bt n\u011bco v\u00edce o t\u00e9to proteinov\u00e9 rodin\u011b a vyzkou\u0161\u00edme, jestli n\u00e1m bioinformatika m\u016f\u017ee pomoci porozum\u011bt jejich biochemii a evoluci.<\/p>\n\n\n\n<p>Za t\u00edmto \u00fa\u010delem vytvo\u0159\u00edme nejd\u0159\u00edve mnoho\u010detn\u00e9 p\u0159i\u0159azen\u00ed proteinov\u00fdch sekvenc\u00ed. To znamen\u00e1, \u017ee vezmeme mnoho aminokyselinov\u00fdch sekvenc\u00ed (kter\u00e9 byste z\u00edskali nap\u0159. zkop\u00edrov\u00e1n\u00edm v\u0161ech v\u00fdsledk\u016f z va\u0161eho BLASTu) a pomoc\u00ed bioinformatick\u00e9ho programu je polo\u017e\u00edme na sebe tak, \u017ee podobn\u00e9 aminokyselinov\u00e9 zbytky a sekven\u010dn\u00ed \u00faseky budou v\u017edy pod sebou.<\/p>\n\n\n\n<p>P\u0159ipraven\u00fd soubor proteinov\u00fdch sekvenc\u00ed naleznete v z\u00e1lo\u017ece &#8220;Sekvence&#8221;. Prvn\u00ed z nich je hov\u011bz\u00ed rhodopsin, se kter\u00fdm jste ji\u017e pracovali v prvn\u00ed \u010d\u00e1sti. K vytvo\u0159en\u00ed mnoho\u010detn\u00e9ho p\u0159i\u0159azen\u00ed pou\u017eijeme n\u00e1sledn\u011b bioinformatick\u00fd n\u00e1stroj EMBL-EBI MUSCLE.<\/p>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-3ca77dbd-92bb-40c5-90ff-80bab24f0706\"><h2>Va\u0161e \u00faloha<\/h2>\n<p><strong>Postupujte n\u00e1sledovn\u011b:<\/strong><br><strong>1. <\/strong>Pomoc\u00ed EMBL-EBI MUSCLE vytvo\u0159te mnoho\u010detn\u00e9 p\u0159i\u0159azen\u00ed 24 opsinov\u00fdch sekvenc\u00ed, kter\u00e9 z\u00edsk\u00e1te v z\u00e1lo\u017ece &#8220;Sekvence&#8221;.<br><strong>2.<\/strong> \u0158i\u010fte se instrukcemi v z\u00e1lo\u017ece &#8220;MUSCLE&#8221; a pokuste se odpov\u011bd\u011bt na ot\u00e1zky v z\u00e1lo\u017ece &#8220;Ot\u00e1zky&#8221;.<\/p>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-fb7f8c0d-e668-4b4b-a403-3125a01d76f8\"><h2>Sekvence<\/h2>\n<p>Your input sequences:<\/p>\n\n\n\n<pre class=\"wp-block-preformatted vf-u-text--break\">&gt;Bos_rho\nMNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA<\/pre>\n\n\n\n<pre class=\"wp-block-preformatted vf-u-text--break\">&gt;Homo_rho\nMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA<\/pre>\n\n\n\n<pre class=\"wp-block-preformatted vf-u-text--break\">&gt;Homo_melan\nMNPPSGPRVPPSPTQEPSCMATPAPPSWWDSSQSSISSLGRLPSISPTAPGTWAAAWVPLPTVDVPDHAHYTLGTVILLVGLTGMLGNLTVIYTFCRSRSLRTPANMFIINLAVSDFLMSFTQAPVFFTSSLYKQWLFGETGCEFYAFCGALFGISSMITLTAIALDRYLVITRPLATFGVASKRRAAFVLLGVWLYALAWSLPPFFGWSAYVPEGLLTSCSWDYMSFTPAVRAYTMLLCCFVFFLPLLIIIYCYIFIFRAIRETGRALQTFGACKGNGESLWQRQRLQSECKMAKIMLLVILLFVLSWAPYSAVALVAFAGYAHVLTPYMSSVPAVIAKASAIHNPIIYAITHPKYRVAIAQHLPCLGVLLGVSRRHSRPYPSYRSTHRSTLTSHTSNLSWISIRRRQESLGSESEVGWTHMEAAAVWGAAQQANGRSLYGQGLEDLEAKAPPRPQGHEAETPGKTKGLIPSQDPRM<\/pre>\n\n\n\n<pre class=\"wp-block-preformatted vf-u-text--break\">&gt;Octopus_rho\nMVESTTLVNQTWWYNPTVDIHPHWAKFDPIPDAVYYSVGIFIGVVGIIGILGNGVVIYLFSKTKSLQTPANMFIINLAMSDLSFSAINGFPLKTISAFMKKWIFGKVACQLYGLLGGIFGFMSINTMAMISIDRYNVIGRPMAASKKMSHRRAFLMIIFVWMWSIVWSVGPVFNWGAYVPEGILTSCSFDYLSTDPSTRSFILCMYFCGFMLPIIIIAFCYFNIVMSVSNHEKEMAAMAKRLNAKELRKAQAGASAEMKLAKISMVIITQFMLSWSPYAIIALLAQFGPAEWVTPYAAELPVLFAKASAIHNPIVYSVSHPKFREAIQTTFPWLLTCCQFDEKECEDANDAEEEVVASERGGESRDAAQMKEMMAMMQKMQAQQAAYQPPPPPQGYPPQGYPPQGAYPPPQGYPPQGYPPQGYPPQGYPPQGAPPQVEAPQGAPPQGVDNQAYQA<\/pre>\n\n\n\n<pre class=\"wp-block-preformatted vf-u-text--break\">&gt;Mizuhopecten_Gqops\nMADNKSTLPGLPDINGTLNRSMTPNTGWEGPYDMSVHLHWTQFPPVTEEWHYIIGVYITIVGLLGIMGNTTVVYIFSNTKSLRSPSNLFVVNLAVSDLIFSAVNGFPLLTVSSFHQKWIFGSLFCQLYGFVGGVFGLMSINTLTAISIDRYVVITKPLQASQTMTRRKVHLMIVIVWVLSILLSIPPFFGWGAYIPEGFQTSCTFDYLTKTARTRTYIVVLYLFGFLIPLIIIGVCYVLIIRGVRRHDQKMLTITRSMKTEDARANNKRARSELRISKIAMTVTCLFIISWSPYAIIALIAQFGPAHWITPLVSELPMMLAKSSSMHNPVVYALSHPKFRKALYQRVPWLFCCCKPKEKADFRTSVCSKRSVTRTESVNSDVSSVISNLSDSTTTLGLTSEGATRANRETSFRRSVSIIKGDEDPCTHPDTFLLAYKEVEVGNLFDMTDDQNRRDSNLHSLYIPTRVQHRPTTQSLGTTPGGVYIVDNGQRVNGLTFNS<\/pre>\n\n\n\n<pre class=\"wp-block-preformatted vf-u-text--break\">&gt;Drosophila_rh6\nMASLHPPSFAYMRDGRNLSLAESVPAEIMHMVDPYWYQWPPLEPMWFGIIGFVIAILGTMSLAGNFIVMYIFTSSKGLRTPSNMFVVNLAFSDFMMMFTMFPPVVLNGFYGTWIMGPFLCELYGMFGSLFGCVSIWSMTLIAYDRYCVIVKGMARKPLTATAAVLRLMVVWTICGAWALMPLFGWNRYVPEGNMTACGTDYFAKDWWNRSYIIVYSLWVYLTPLLTIIFSYWHIMKAVAAHEKAMREQAKKMNVASLRNSEADKSKAIEIKLAKVALTTISLWFFAWTPYTIINYAGIFESMHLSPLSTICGSVFAKANAVCNPIVYGLSHPKYKQVLREKMPCLACGKDDLTSDSRTQATAEISESQA<\/pre>\n\n\n\n<pre class=\"wp-block-preformatted vf-u-text--break\">&gt;Drosophila_rh2\nMERSHLPETPFDLAHSGPRFQAQSSGNGSVLDNVLPDMAHLVNPYWSRFAPMDPMMSKILGLFTLAIMIISCCGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMASQSPVMIINFYYETWVLGPLWCDIYAGCGSLFGCVSIWSMCMIAFDRYNVIVKGINGTPMTIKTSIMKILFIWMMAVFWTVMPLIGWSAYVPEGNLTACSIDYMTRMWNPRSYLITYSLFVYYTPLFLICYSYWFIIAAVAAHEKAMREQAKKMNVKSLRSSEDCDKSAEGKLAKVALTTISLWFMAWTPYLVICYFGLFKIDGLTPLTTIWGATFAKTSAVYNPIVYGISHPKYRIVLKEKCPMCVFGNTDEPKPDAPASDTETTSEADSKA<\/pre>\n\n\n\n<pre class=\"wp-block-preformatted vf-u-text--break\">&gt;Xenopus_melanops\nMDLGKTVEYGTHRQDAIAQIDVPDQVLYTIGSFILIIGSVGIIGNMLVLYAFYRNKKLRTAPNYFIINLAISDFLMSATQAPVCFLSSLHREWILGDIGCNVYAFCGALFGITSMMTLLAISINRYIVITKPLQSIQWSSKKRTSQIIVLVWMYSLMWSLAPLLGWSSYVPEGLRISCTWDYVTSTMSNRSYTMMLCCCVFFIPLIVISHCYLFMFLAIRSTGRNVQKLGSYGRQSFLSQSMKNEWKMAKIAFVIIIVFVLSWSPYACVTLIAWAGHGKSLTPYSKTVPAVIAKASAIYNPIIYGIIHPKYRETIHKTVPCLRFLIREPKKDIFESSVRGSIYGRQSASRKKNSFISTVSTAETVSSHIWDNTPNGHWDRKSLSQTMSNLCSPLLQDPNSSHTLEQTLTWPDDPSPKEILLPSSLKSVTYPIGLESIVKDEHTNNSCVRNHRVDKSGGLDWIINATLPRIVIIPTSESNISETKEEHDNNSEEKSKRTEEEEDFFNFHVDTSLLNLEGLNSSTDLYEVVERFLS<\/pre>\n\n\n\n<pre class=\"wp-block-preformatted vf-u-text--break\">&gt;Platynereis_rops\nMSRSEVLVPGSMSLDGLLTTAHPIGNDSIETILHPYWQQFDIENTIPDSWHYAVAAWMTFFGILGVSGNLLVVWTFLKTKSLRTAPNMLLVNLAIGDMAFSAINGFPLLTISSINKRWVWGKLWRELYAFVGGIFGLMSINTLAWIAIDRFYVITNPLGAAQTMTKKRAFIILTIIWANASLWALAPFFGWGAYIPEGFQTSCTYDYLTQDMNNYTYVLGMYLFGFIFPVAIIFFCYLGIVRAIFAHHAEMMATAKRMGANTGKADADKKSEIQIAKVAAMTIGTFMLSWTPYAVVGVFGMIKPHSEMFIHPLLAEIPVMMAKASARYNPIIYALSHPKFRAEIDKHFPWLLCCCKPKPKAQLPSSTTKGSIASKTEADTSV<\/pre>\n\n\n\n<pre class=\"wp-block-preformatted vf-u-text--break\">&gt;Danio_melanops\nMSHHSSWRGHHCAPGDINCTAGFKESLGSRNYKLLHVPVHGPTHSHHHDPPHPFPTVDVPDHAHYIIGSVILIVGITGVIGNALVVYVFCRSRTLRTAGNMFIVNLAVADFLMSVTQSPVFFAASLHRRWVFGERPCELYAFCGALFGICSMMTLTAIAADRCLAITQPLALVSRVSRRKAGAVFVVVWLYSLGWSLPPFFGWSAYVPEGLQTSCSWDYMTFTPSVRAYTILLFVFVFFIPLGIIGSCYFAIFQTIRAAGKEIRELDCGETHKVYERMQNEWKMAKVALVVILLFIISWSPYSVVALTATAGYSHFLTPYMNSVPAVIAKASAIHNPIIYAITHPKYRVAIARYIPVLRPILRVKEKDLRSSFSSGSVSSRRPTLTSHQCSLGVSMGNAARANGRWGKTRLSSASDSDSCWTESEADGSSVSSLTFGRRVSTEISTDTVILSPGSSVSNASGQKSERAHKVVSVPVPSITFETDAADGESLSDGKALLGGN<\/pre>\n\n\n\n<pre class=\"wp-block-preformatted vf-u-text--break\">&gt;Sepia_rho\nMGRDIPDNETWWYNPTMEVHPHWKQFNQVPDAVYYSLGIFIGICGIIGCTGNGIVIYLFTKTKSLQTPANMFIINLAFSDFTFSLVNGFPLMTISCFIKKWVFGMAACKVYGFIGGIFGLMSIMTMSMISIDRYNVIGRPMAASKKMSHRRAFLMIIFVWMWSTLWSIGPIFGWGAYVLEGVLCNCSFDYITRDSATRSNIVCMYIFAFCFPILIIFFCYFNIVMAVSNHEKEMAAMAKRLNAKELRKAQAGASAEMKLAKISIVIVTQFLLSWSPYAVVALLAQFGPIEWVTPYAAQLPVMFAKASAIHNPLIYSVSHPKFREAIAENFPWIITCCQFDEKEVEDDKDAETEIPATEQSGGESADAAQMKEMMAMMQKMQQQQAAYPPQGAYPPQGGYPPQGYPPPPAQGGYPPQGYPPPPQGYPPAQGYPPQGYPPPQGAPPQGAPPQAAPPQGVDNQAYQA<\/pre>\n\n\n\n<pre class=\"wp-block-preformatted vf-u-text--break\">&gt;Takifugu_TMT\nMIVSNVSLSGCAGVNGAVCAAEGHQAGGSDRSTLTPTGNLVVSVFLGFIGTFGLVNNLLVLVLFCRYKMLRSPINLLLMNISISDLLVCVLGTPFSFAASTQGRWLIGEAGCVWYGFANSLFGVVSLISLAVLSFERYSTMMTPTEADPSNYCKVCLGITLSWVYSLVWTVPPLFGWSSYGPEGPGTTCSVNWTAKTTNSISYIICLFVFCLIVPFLVIVFCYGKLLCAIRQVSGINASTSRKREQRVLCMVVIMVICYLLCWLPYGVVALLATFGPPDLVTPEASIIPSVLAKSSTVINPIIYVFMNKQFYRCFLALLCCQDPRSGSSMKSSSKVATKAKGVTPTGQRRTDLLYMVASLGRPAATIPQLGPSFDATNDFTKPPSSDTIKPVVVSLAAHCDG<\/pre>\n\n\n\n<pre class=\"wp-block-preformatted vf-u-text--break\">&gt;Gallus_LWops\nMSSNSSQAPPNGTPGPFDGPQWPYQAPQSTYVGVAVLMGTVVACASVVNGLVIVVSICYKKLRSPLNYILVNLAVADLLVTLCGSSVSLSNNINGFFVFGRRMCELEGFMVSLTGIVGLWSLAILALERYVVVCRPLGDFQFQRRHAVSGCAFTWGWALLWSTPPLLGWSSYVPEGLRTSCGPNWYTGGSNNNSYILSLFVTCFVLPLSLILFSYTNLLLTLRAAAAQQKEADTTQRAEREVTRMVIVMVMAFLLCWLPYSTFALVVATHKGIIIQPVLASLPSYFSKTATVYNPIIYVFMNKQFQSCLLEMLCCGYQPQRTGKASPGTPGPHADVTAAGLRNKVMPAHPV<\/pre>\n\n\n\n<pre class=\"wp-block-preformatted vf-u-text--break\">&gt;Xenopus_Parietops\nMDGNSTTPGIAVNLTVMPTIFPRSGYSILSFLMFLNAVFSICNNAIVILVTLKHPQLRNPINIFILNLSFSDLMMALCGTTIVVSTNYHGYFYLGKQFCIFQGFAVNYFGIVSLWSLTLLAYERYNVVCEPIGALKLSTKRGYQGLVFIWLFCLFWAIAPLFGWSSYGPEGVQTSCSIGWEERSWSNYSYIISYFLTCFIIPVGIIGFSYGSILRSLHQLNRKIEQQGGKTNPREEKRVVIMVLFMVLAFLICWLPYTVFALIVVINPQLYISPLAATLPTYFAKTSPVYNPIIYIFLNKQFRTYAVQCLTCGHINLDSLEEDTESVSAQAENMLTPKTNQVAPA<\/pre>\n\n\n\n<pre class=\"wp-block-preformatted vf-u-text--break\">&gt;Danio_MW4\nMNGTEGNNFYIPLSNRTGLARSPYEYPQYYLAEPWQFKLLAVYMFFLICLGFPINGLTLLVTAQHKKLRQPLNFILVNLAVAGTIMVCFGFTVTFYTAINGYFVLGPTGCAIEGFMATLGGEVALWSLVVLAVERYIVVCKPMGSFKFSASHAFAGCAFTWVMAMACAAPPLVGWPRYIPEGMQCSCGPDYYTLNPEYNNESYVLYMFICHFILPVTIIFFTYGRLVCTVKAAAAQQQESESTQKAEREVTRMVILMVLGFLIAWTPYATVAAWIFFNKGAAFSAQFMAVPAFFSKTSALYNPVIYVLLNKQFRNCMLTTLFCGKNPLGDDESSTVSTSKTEVSSVSPA<\/pre>\n\n\n\n<pre class=\"wp-block-preformatted vf-u-text--break\">&gt;Danio_extraocular\nMNGTEGPNFYVPMSNRTGLVRSPFEEPQYYLAEPWQFSLLAAYMLFLILGSFPINALTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTVTLYTALHGYFLLGVTGCNIEGFFATLGGEIALWSLVVLAIERYIVVCKPMSTFRFGEKHAIIGVGFTWVMALTCAVPPLLGWSRYIPEGMQCSCGIDYYTPKPEVHNTSFVIYMFILHFSIPLLIIFFCYSRLLCTVRAAAAQQQESETTQRAEREVTRMVVVMVIAFLVCWVPYASVAWYIFANQGAEFGPVFMTVPAFFAKSAALYNPVIYIMLNRQFRNCMLSTVCCGKNPLAEDESSSAVSSKTQSSVVSSAQVSPA<\/pre>\n\n\n\n<pre class=\"wp-block-preformatted vf-u-text--break\">&gt;Latimeria_Rh2\nMNGTEGMNFYVPLSNRTGLVRSPFEYTQYYLAEPWKFSVLCAYMFLLIILGFPINFLTLLVTFKHKKLRQPLNYILVNLAVASLFMVVFGFTVTFYSSLNGYFVLGPMGCAMEGFFATLGGQVALWSLVVLAIERYIVVCKPMGNFRFASSHAIMGIAFTWIMALACAAPPLVGWSRYIPEGLQCSCGPDYYTLNPDFHNESYVMYLFLVHFLLPIIIIFFTYGRLICKVKEAAAQQQESASTQKAEKEVTRMVILMVIGFLTAWVPYASAAFWIFCNRGAEFTATLMTVPAFFSKSSCLFNPIIYVLLNKQFRNCMITTLCCGKNPLGDDDTSSAVSQSKTDVSSVSSSQVSPA<\/pre>\n\n\n\n<pre class=\"wp-block-preformatted vf-u-text--break\">&gt;Xenopus_green_ops\nMSKGRPDLRMEMPDEFYVPIPLETTNISSLSPFLVPQTHLGTPGIFMSISAFMLFTIIFGFPLNLLTIICTVKYKKLRSHLNYILVNLAVANLIVICFGSTTAFYSFSQMYFSLGTLACKIEGFTATLGGIIGLWSLAVVAFERFLVICKPMGNFTFRESHAVLGCILTWVIGLVAAIPPLLGWSRYIPEGLQCSCGPDWYTVNNKWNNESYVLFLFCFCFGFPLAIIVFSYGRLLLALHAVAKQQEQSATTQKAEREVTRMVIVMVVGFLVCWLPYASFALWAVTHRGELFDLRMSSVPSVFSKASTVYNPFIYIFMNRQFRSCMMKMIFCGKNPLGDDEETSVSGSTQVSSVSSSQIAPS<\/pre>\n\n\n\n<pre class=\"wp-block-preformatted vf-u-text--break\">&gt;Xenopus_violet_ops\nMLEEEDFYLFKNVSNVSPFDGPQYHIAPKWAFTLQAIFMGMVFLIGTPLNFIVLLVTIKYKKLRQPLNYILVNITVGGFLMCIFSIFPVFVSSSQGYFFFGRIACSIDAFVGTLTGLVTGWSLAFLAFERYIVICKPMGNFNFSSSHALAVVICTWIIGIVVSVPPFLGWSRYMPEGLQCSCGPDWYTVGTKYRSEYYTWFIFIFCFVIPLSLICFSYGRLLGALRAVAAQQQESASTQKAEREVSRMVIFMVGSFCLCYVPYAAMAMYMVTNRNHGLDLRLVTIPAFFSKSSCVYNPIIYSFMNKQFRGCIMETVCGRPMSDDSSVSSTSQRTEVSTVSSSQVSPA<\/pre>\n\n\n\n<pre class=\"wp-block-preformatted vf-u-text--break\">&gt;Gallus_blue_ops\nMHPPRPTTDLPEDFYIPMALDAPNITALSPFLVPQTHLGSPGLFRAMAAFMFLLIALGVPINTLTIFCTARFRKLRSHLNYILVNLALANLLVILVGSTTACYSFSQMYFALGPTACKIEGFAATLGGMVSLWSLAVVAFERFLVICKPLGNFTFRGSHAVLGCVATWVLGFVASAPPLFGWSRYIPEGLQCSCGPDWYTTDNKWHNESYVLFLFTFCFGVPLAIIVFSYGRLLITLRAVARQQEQSATTQKADREVTKMVVVMVLGFLVCWAPYTAFALWVVTHRGRSFEVGLASIPSVFSKSSTVYNPVIYVLMNKQFRSCMLKLLFCGRSPFGDDEDVSGSSQATQVSSVSSSHVAPA<\/pre>\n\n\n\n<pre class=\"wp-block-preformatted vf-u-text--break\">&gt;Danio_LWops\nMAEHWGDAIYAARRKGDETTREAMFTYTNSNNTKDPFEGPNYHIAPRWVYNVATVWMFFVVVASTFTNGLVLVATAKFKKLRHPLNWILVNLAIADLGETLFASTISVINQFFGYFILGHPMCIFEGYTVSVCGIAALWSLTVISWERWVVVCKPFGNVKFDAKWASAGIIFSWVWAAAWCAPPIFGWSRYWPHGLKTSCGPDVFSGSEDPGVQSYMVVLMITCCIIPLAIIILCYIAVYLAIHAVAQQQKDSESTQKAEKEVSRMVVVMIFAYCFCWGPYTFFACFAAANPGYAFHPLAAAMPAYFAKSATIYNPVIYVFMNRQFRVCIMQLFGKKVDDGSEVSTSKTEVSSVAPA<\/pre>\n\n\n\n<pre class=\"wp-block-preformatted vf-u-text--break\">&gt;Danio_SWops\nMDAWAVQFGNASKVSPFEGEQYHIAPKWAFYLQAAFMGFVFIVGTPMNGIVLFVTMKYKKLRQPLNYILVNISLAGFIFDTFSVSQVSVCAARGYYSLGYTLCSMEAAMGSIAGLVTGWSLAVLAFERYVVICKPFGSFKFGQGQAVGAVVFTWIIGTACATPPFFGWSRYIPEGLGTACGPDWYTKSEEYNSESYTYFLLITCFMMPMTIIIFSYSQLLGALRAVAAQQAESESTQKAEREVSRMVVVMVGSFVLCYAPYAVTAMYFANSDEPNKDYRLVAIPAFFSKSSSVYNPLIYAFMNKQFNACIMETVFGKKIDESSEVSSKTETSSVSA<\/pre>\n\n\n\n<pre class=\"wp-block-preformatted vf-u-text--break\">&gt;Homo_MWops\nMAQQWSLQRLAGRHPQDSYEDSTQSSIFTYTNSNSTRGPFEGPNYHIAPRWVYHLTSVWMIFVVIASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIASTISVVNQVYGYFVLGHPMCVLEGYTVSLCGITGLWSLAIISWERWMVVCKPFGNVRFDAKLAIVGIAFSWIWAAVWTAPPIFGWSRYWPHGLKTSCGPDVFSGSSYPGVQSYMIVLMVTCCITPLSIIVLCYLQVWLAIRAVAKQQKESESTQKAEKEVTRMVVVMVLAFCFCWGPYAFFACFAAANPGYPFHPLMAALPAFFAKSATIYNPVIYVFMNRQFRNCILQLFGKKVDDGSELSSASKTEVSSVSSVSPA<\/pre>\n\n\n\n<pre class=\"wp-block-preformatted vf-u-text--break\">&gt;Danio_mel_rec1A\nMFMNGSSLNSSALDPSEQALQRPPWVTTTLGCFLIFTIVVDILGNLLVIFSVYRNKKLQNAGNIFVVSLAVADLVVAIYPYPLVLTSIFHRGWNLGYMHCQISGFLMGVSVIGSIFNITGIAINCYCYICHSLKYDKLYSDKNSVCYVLLIWALTVLAIVPNLFVGSLQYDPRVYSCTFEQSASSAYTIAVVFFHFILPIMIVTYCYLRIWVLVIQVRRRVKPDNRPKITPHDVRNFVTMFVVFVLFAVCWAPLNFIGLAVAISPERVVPLIPEWLFVASYFMAYFNSCLNAIVYGVLNQNFRREYKRIVVSVCTARIFFGESSNEAQERLKSKPSPLMTNNNQVKVDSV<\/pre>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-49802ed2-ad8e-4020-8ef1-38a6e6070f30\"><h2>MUSCLE<\/h2>\n<p><strong>1.<\/strong> Zkop\u00edrujte a vlo\u017ete v\u0161echny aminokyselinov\u00e9 sekvence (v\u010detn\u011b n\u00e1zvu a znam\u00e9nka &#8220;&gt;&#8221;) najednou do pol\u00ed\u010dka vstupn\u00edch sekvenc\u00ed (viz n\u00ed\u017ee). P\u0159\u00edpadn\u011b m\u016f\u017eete nahr\u00e1t <a href=\"http:\/\/emblog.embl.de\/ells\/wp-content\/uploads\/2014\/01\/FASTA_Opsins_part2.txt\" target=\"_blank\" rel=\"noreferrer noopener\">FASTA soubor<\/a>, kter\u00fd obsahuje dan\u00e9 sekvence, p\u0159\u00edmo z va\u0161eho po\u010d\u00edta\u010de.<\/p>\n\n\n\n<p><strong>2.<\/strong> Jako v\u00fdstupn\u00ed form\u00e1t (Output format) vyberte ClustalX.<\/p>\n\n\n\n<p><strong>3.<\/strong> Klikn\u011bte na tla\u010d\u00edtko &#8220;Submit&#8221;.<\/p>\n\n\n\n<p><strong>4.<\/strong> Po chvilce je vytvo\u0159eno mnoho\u010detn\u00e9 p\u0159i\u0159azen\u00ed v\u0161ech opsinov\u00fdch sekvenc\u00ed. V\u00fdsledky si m\u016f\u017eete prohl\u00e9dnout v z\u00e1lo\u017ece &#8220;Alignment&#8221;, pro lep\u0161\u00ed zobrazen\u00ed doporu\u010dujeme kliknout na &#8220;Show colors&#8221;.<\/p>\n\n\n\n<p><strong>5.<\/strong> Pro pokro\u010dilej\u0161\u00ed anal\u00fdzu mus\u00edme pou\u017e\u00edt program JalView, s jeho\u017e pomoc\u00ed m\u016f\u017eeme mnoho\u010detn\u00e9 p\u0159i\u0159azen\u00ed editovat. Klikn\u011bte prav\u00fdm tla\u010d\u00edtkem &#8220;Results Summary&#8221; a otev\u0159ete je v dal\u0161\u00ed z\u00e1lo\u017ece internetov\u00e9ho prohl\u00ed\u017ee\u010de (&#8220;Open Link in New Tab&#8221;). V t\u00e9to nov\u00e9 z\u00e1lo\u017ece prohl\u00ed\u017ee\u010de pak otev\u0159ete alignment pomoc\u00ed &#8220;JalView&#8221;. (Otev\u0159en\u00ed nov\u00e9 z\u00e1lo\u017eky prohl\u00ed\u017ee\u010de jsme d\u011blali proto, aby okno JalView z\u016fstalo otev\u0159en\u00e9 nez\u00e1visle na dal\u0161\u00edch kroc\u00edch. S dal\u0161\u00edmi kroky \u00falohy m\u016f\u017eete pokra\u010dovat v p\u016fvodn\u00ed z\u00e1lo\u017ece prohl\u00ed\u017ee\u010de).<\/p>\n\n\n\n<p class=\"has-text-align-left\"><strong><strong>6.<\/strong> <\/strong>Ujist\u011bte se, \u017ee v\u00e1\u0161 alignment obsahuje v\u0161ech 24 sekvenc\u00ed (p\u0159\u00edpadn\u011b m\u016f\u017eete i rozt\u00e1hnout okno JalView do v\u00fd\u0161ky za prav\u00fd doln\u00ed roh).<\/p>\n\n\n\n<div class=\"wp-block-image wp-image-4943\"><figure class=\"vf-figure  | vf-figure--align vf-figure--align-inline-end  size-large\"><img loading=\"lazy\" decoding=\"async\" width=\"435\" height=\"203\" class=\"vf-figure__image\" src=\"https:\/\/www.embl.org\/ells\/wp-content\/uploads\/2021\/05\/HydrophobicityScale_Web.png\" alt=\"\" class=\"wp-image-1439\" srcset=\"https:\/\/www.embl.org\/ells\/wp-content\/uploads\/2021\/05\/HydrophobicityScale_Web.png 435w, https:\/\/www.embl.org\/ells\/wp-content\/uploads\/2021\/05\/HydrophobicityScale_Web-300x140.png 300w\" sizes=\"auto, (max-width: 435px) 100vw, 435px\" \/><figcaption class=\"vf-figure__caption\">Hydrophobicity Scale<\/figcaption><\/figure><\/div>\n\n\n\n<div class=\"wp-block-image wp-image-4944\"><figure class=\"vf-figure  | vf-figure--align vf-figure--align-inline-end  size-large\"><img loading=\"lazy\" decoding=\"async\" width=\"170\" height=\"157\" class=\"vf-figure__image\" src=\"https:\/\/www.embl.org\/ells\/wp-content\/uploads\/2021\/05\/IdentityScale_Web.png\" alt=\"\" class=\"wp-image-1440\"\/><figcaption class=\"vf-figure__caption\">Identity Scale<\/figcaption><\/figure><\/div>\n\n\n\n<p>V okn\u011b JalView m\u016f\u017eete vybrat r\u016fzn\u00e1 krit\u00e9ria pro zv\u00fdrazn\u011bn\u00ed mnoho\u010detn\u00e9ho p\u0159i\u0159azen\u00ed (v\u0161e najdete pod z\u00e1lo\u017ekou &#8220;Colour&#8221;). M\u016f\u017eete nap\u0159. zvolit barevn\u00e9 zv\u00fdrazn\u011bn\u00ed podle procent identity \u010di na z\u00e1klad\u011b hydrofobicity aminokyselin.<\/p>\n\n\n\n<p><strong>7.<\/strong> Dole v okn\u011b JalView jsou zobrazena sk\u00f3re mnoho\u010detn\u00e9ho p\u0159i\u0159azen\u00ed v podob\u011b sloupc\u016f odr\u00e1\u017eej\u00edc\u00edch toto\u017enost\/podobnost. Pozorujete n\u011bjak\u00e9 zvl\u00e1\u0161tnosti \u010di n\u00e1padn\u00e9 vzorce? Pokuste se odpov\u011bd\u011bt na ot\u00e1zky v z\u00e1lo\u017ece &#8220;Ot\u00e1zky&#8221;.<\/p>\n\n\n\n<p><strong>Pozor:<\/strong> nezav\u00edrejte okno JalView po skon\u010den\u00ed t\u00e9to \u010d\u00e1sti \u00falohy, jeliko\u017e jej budeme je\u0161t\u011b pot\u0159ebovat.<\/p>\n\n\n<div\n  class=\"vf-embed vf-embed--custom-ratio\"\n\n  style=\"--vf-embed-max-width: 100%;\n    --vf-embed-custom-ratio-x: 640;\n    --vf-embed-custom-ratio-y: 360;\"\n><iframe loading=\"lazy\" width=\"640\" height=\"360\" src=\"https:\/\/www.ebi.ac.uk\/Tools\/msa\/muscle\/\" frameborder=\"0\" allow=\"accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture\" allowfullscreen><\/iframe><\/div>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-f3293f44-6770-44b4-aa21-2e837496da09\"><h2>Ot\u00e1zky<\/h2>\n<p><strong>1.<\/strong> Co m\u016f\u017eete usoudit z va\u0161eho mnoho\u010detn\u00e9ho p\u0159i\u0159azen\u00ed?<br><strong>2.<\/strong> Pozorujete n\u011bjak\u00e9 \u00faseky sekvenc\u00ed, kter\u00e9 jsou si podobn\u011bj\u0161\u00ed ne\u017e jin\u00e9. Jestli ano, kolik? Jak\u00e9 biochemick\u00e9 povahy jsou tyto v\u00edce podobn\u00e9 (konzervovan\u00e9) \u00faseky (jsou sp\u00ed\u0161e z\u00e1sadit\u00e9, kysel\u00e9, hydrofobn\u00ed \u010di hodrofiln\u00ed&#8230;?)<br><strong>3.<\/strong> Naleznete n\u011bjak\u00e9 vysoce konzervovan\u00e9 (p\u0159\u00edtomn\u00e9 v drtiv\u00e9 v\u011bt\u0161in\u011b) aminokyselinov\u00e9 zbytky \u010di kr\u00e1tk\u00e9 motivy p\u0159\u00edtomn\u00e9 ve v\u0161ech opsinov\u00fdch sekvenc\u00edch? Pozor, jedna ze sekvenc\u00ed &#8211; &#8220;Danio_mel_rec1A&#8221; &#8211; nen\u00ed opsin, n\u00fdbr\u017e pouze jemu evolu\u010dn\u011b bl\u00edzk\u00e1 molekula, kterou m\u00e1me v alignmentu jen pro pozd\u011bj\u0161\u00ed \u00fa\u010dely. Pro tento bod \u00falohy ji proto pros\u00edm ignorujte.<\/p>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-52f5c833-db34-493c-919c-efbbcbcdb5cc\"><h2>Activity navigation<\/h2>\n<ul class=\"wp-block-list\"><li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/opsins-bioinformatics\/?lang=cs\" data-type=\"teachingbase\" data-id=\"28420\">P\u00e1tr\u00e1n\u00ed po evoluci sv\u011btlo\u010divn\u00fdch protein\u016f<\/a><\/li><li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/opsins-bioinformatics\/part-1-search-for-protein-identity\/?lang=cs\" data-type=\"teachingbase\" data-id=\"28440\">\u010c\u00e1st 1: Hled\u00e1n\u00ed identity nezn\u00e1m\u00e9ho proteinu<\/a><\/li><li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/opsins-bioinformatics\/part-2-multiple-sequence-alignment-of-protein-sequences\/?lang=cs\" data-type=\"teachingbase\" data-id=\"28454\">Part 2: Multiple sequence alignment of protein sequences<\/a><\/li><li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/opsins-bioinformatics\/part-3-phylogenetic-analysis-of-aligned-protein-sequences\/?lang=cs\" data-type=\"teachingbase\" data-id=\"28474\"><strong>\u010c\u00e1st 3: Fylogenetick\u00e1 anal\u00fdza proteinov\u00fdch sekvenc\u00ed<\/strong><\/a><\/li><li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/opsins-bioinformatics\/part-4-topological-and-structural-analysis-of-proteins\/?lang=cs\" data-type=\"teachingbase\" data-id=\"28497\">\u010c\u00e1st 4: Topologick\u00e1 a strukturn\u00ed anal\u00fdza protein\u016f<\/a><\/li><\/ul>\n<\/section>\n<\/div><\/div>\n\n\n\n<p><\/p>\n\n\n\n<p><\/p>\n<\/div><\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"featured_media":28455,"parent":28420,"menu_order":3,"template":"","class_list":["post-28454","teachingbase","type-teachingbase","status-publish","has-post-thumbnail","hentry"],"acf":[],"_links":{"self":[{"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/teachingbase\/28454","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/teachingbase"}],"about":[{"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/types\/teachingbase"}],"up":[{"embeddable":true,"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/teachingbase\/28420"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/media\/28455"}],"wp:attachment":[{"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/media?parent=28454"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}