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Algorithmic Bioinformatics Michael Schroeder BioTechnological Center TU Dresden Biotec Bioinformatics cycle Applied bioinformatics Use bioinformatics tools Access databases and tools over the web Programming for bioinformatics Learn programming skills relevant to bioinformatics Algorithmic bioinformatics Develop bioinformatics tools By Michael Schroeder, Biotec 2 Syllabus The module covers algorithms and data structures for bioinformatics. It will cover: sequences (DNA and amino acid sequences). structure (structure comparison and alignment) For each of these data types the module will cover important algorithms to manipulate and analyse the data. Students will appreciate the different types of data mostly generated in bioinformatics Students will understand how to analyse the different types of data Students will be able to design data structures and algorithms to analysis bioinformatics data Students will be able to critically assess quality of algorithms Students will be able to write basic programmes By Michael Schroeder, Biotec 3 Book Protein Bioinformatics by Eidhammer et al. Chapters on sequence alignment, multiple sequence alignment, and structure alignment By Michael Schroeder, Biotec 4 Structure of module Algorithms for Sequences Sequence comparison Multiple sequence alignment Algorithms for Structures Intro to structures Superposition Geometric techniques Clustering Advanced topics Good news: Conceptually You know most of the topics We will cover Bad news: It’s a long way to understand all the details Scoppi and Interaction interfaces HMM and prediction of interactions Structure prediction Docking Atomic force microscopy and bioinformatics Textmining Revision By Michael Schroeder, Biotec 5 Labs Annalisa and Frank will run the labs. If you have any questions then contact him on: [email protected] Style Programming, paper and pencil, use programmes By Michael Schroeder, Biotec 6 Lab Contents Local and global sequence alignments Phylogeny and clustering Finding and highlighting sequence motifs in PDB structures Distance plots for inter-atomic distances (Using programmes for docking, molecular modelling, gene expression data analysis, textmining) By Michael Schroeder, Biotec 7 Assessment Lecture: Exam, which counts 80% Lab: Programming task in pairs 20% Will be handed out during term By Michael Schroeder, Biotec 8 Assessment Homework is mandatory! Each 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 Handing in of homework is pre-requisite for the programming task no homework = no marks By Michael Schroeder, Biotec 9 Preparation for labs and lectures Get Book Read Book Read all slides from term 1 again Read all slides from term 2 again Do all programming labs of term 2 again, especially Dot plots Sequence alignments Residue counts By Michael Schroeder, Biotec 10