Předmět Bioinformatika II – proteiny (Bi9060)

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Materiál	Typ	Datum	Počet stažení

Cíl

The aim of this course is to give an introduction to Bioinformatics. The course will consist of theoretical part followed by practical training using computers and Internet. An introduction will be given to the theory of genome and protein information resources, to the DNA and protein sequence analysis, to the organization and searching of primary and secondary databases, etc. The students will be able to understand the basic principles of bioinformatics and to use basic tools and databases for solving practical problems. They will be able to handle different types of data by analogy with examples learned during the course.

Osnova

I. OPENINGwhat is it Bioinformatics?study materialorganizationlecturesexaminationII. INTRODUCTIONhistory of sequencingwhat is it Bioinformatics?sequence to structure deficitgenome projectswhy is Bioinformatics important?patter recognition and predictionfolding problemsequence analysishomo/analogy and ortho/paralogyIII. INFORMATION NETWORKSwhat is the Internet?how do computers find each other?FTP and Telnetwhat is the World Wide Web?HTTP, HTML and URLEMBnet, EBI, NCBISRS and ENTREZIV. PROTEIN INFORMATION RESOURCES-Ibiological databases - introductionprimary protein sequence databasescomposite protein sequence databasesV. PROTEIN INFORMATION RESOURCES-IIsecondary databasescomposite secondary databasesprotein structure databasesprotein structure classification databasesVI. GENOME INFORMATION RESOURCESprimary DNA sequence databasesspecialised DNA sequence databasesVII. DNA SEQUENCE ANALYSISwhy to analyse DNA?gene structuregene sequence analysisexpression profile, cDNA, ESTEST sequences analysisVIII. PAIRWISE SEQUENCE ALIGNMENTdatabase searchingalphabets and complexityalgorithms and programssequences and sub-sequencesidentity and similaritydotplotlocal and global similaritypairwise database searchingIX. MULTIPLE SEQUENCE ALIGNMENTmultiple sequence alignmentconsensus sequencemanual methodssimultaneous and progressive methodsdatabases of multiple sequence alignmentshybrid approach for database searchingX. SECONDARY DATABASE SEARCHINGwhy to search secondary databases?secondary databasesregular expressionsfingerprintsblocksprofilesHidden Markov ModelsXI. ANALYSIS PACKAGEScommercial databasescommercial softwarecomprehensive packagespackages for DNA analysisintranet packagesInternet packagesXII. PROTEIN STRUCTURE MODELLINGprotein structureprotein structure databasesprediction of secondary structureprediction of protein foldprediction of tertiary structuremodelling of protein-ligand complexesXIII. BIOINFORMATICS IN PRACTICE-IInformation networksProtein information resourcesGenome information resourcesDNA sequence analysisXIV. BIOINFORMATICS IN PRACTICE-IIPairwise sequence alignmentMultiple sequence alignmentSecondary database searchingProtein structure modelling

Literatura

Introduction to Bioinformatics, T.K. Attwood & D.J. Parry-Smith, Longman, Essex, 1999.

Požadavky

( Bi4010 Základy molekulární biologie || Bi4020 Molekulární biologie ) && ( NOW ( Bi5000 Bioinformatika I ) || SOUHLAS ) && ! C9080 Bioinformatics

Garant

prof. Mgr. Jiří Damborský, Dr.

Vyučující

prof. Mgr. Jiří Damborský, Dr.Mgr. Martina Damborskádoc. RNDr. Roman Pantůček, Ph.D.Mgr. Eva Šebestová, Ph.D.