Michael Schroeder BioTechnological Center TU Dresden Biotec Algorithmic Bioinformatics

By Michael Schroeder, Biotec2 Bioinformatics cycle nApplied bioinformatics nUse bioinformatics tools nAccess databases and tools over the web nProgramming for bioinformatics nLearn programming skills relevant to bioinformatics nAlgorithmic bioinformatics nDevelop bioinformatics tools

By Michael Schroeder, Biotec3 Syllabus nThe module covers algorithms and data structures for bioinformatics. It will cover: nsequences (DNA and amino acid sequences). nstructure (structure comparison and alignment) nFor each of these data types the module will cover important algorithms to manipulate and analyse the data. n nStudents will appreciate the different types of data mostly generated in bioinformatics nStudents will understand how to analyse the different types of data nStudents will be able to design data structures and algorithms to analysis bioinformatics data nStudents will be able to critically assess quality of algorithms nStudents will be able to write basic programmes

By Michael Schroeder, Biotec4 Book nProtein Bioinformatics by Eidhammer et al. nChapters on nsequence alignment, nmultiple sequence alignment, and nstructure alignment

By Michael Schroeder, Biotec5 Structure of module nAlgorithms for Sequences nSequence comparison nMultiple sequence alignment nAlgorithms for Structures nIntro to structures nSuperposition nGeometric techniques nClustering nAdvanced topics nScoppi and Interaction interfaces nHMM and prediction of interactions nStructure prediction nDocking nAtomic force microscopy and bioinformatics nTextmining nRevision Good news: Conceptually You know most of the topics We will cover Bad news: It’s a long way to understand all the details

By Michael Schroeder, Biotec6 Labs nAnnalisa and Frank will run the labs. nIf you have any questions then contact him on: nStyle nProgramming, npaper and pencil, nuse programmes

By Michael Schroeder, Biotec7 Lab Contents nLocal and global sequence alignments nPhylogeny and clustering nFinding and highlighting sequence motifs in PDB structures nDistance plots for inter-atomic distances n(Using programmes for docking, molecular modelling, gene expression data analysis, textmining)

By Michael Schroeder, Biotec8 Assessment nLecture: Exam, which counts 80% nLab: nProgramming task in pairs 20% nWill be handed out during term

By Michael Schroeder, Biotec9 Assessment nHomework is mandatory! nEach week you will be given tasks to complete for the following week. You will not be marked on the homework, but you must hand it in nHanding in of homework is pre-requisite for the programming task nno homework = no marks

By Michael Schroeder, Biotec10 Preparation for labs and lectures nGet Book nRead Book nRead all slides from term 1 again nRead all slides from term 2 again nDo all programming labs of term 2 again, especially nDot plots nSequence alignments nResidue counts