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BIF601 : Bioinformatics Computing I

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Course Info

Course Category

Bioinformatics

Course Level

Undergraduate

Credit Hours

3

Pre-requisites

N/A

Instructor

Dr. Muhammad Usman Ghani Khan
Ph.D. in Computer Science
The University of Sheeld, UK, 2012

Course Contents

Database, Database Advantages, Data Management, Database Software, Computer Network, Data Communication, Data communication, Communication tasks and protocols,Topology, Topology and Transmission modes, Geographical Scope and Communication Models, Communication Models and transmission Technology, Communication Models and transmission Technology, Communication Models and transmission Technology, Bandwidth/Frequency Spectrum, Network Security, Information retrieval and Search engines, information retrieval introduction, IRModels, R evaluation Measures, R in Biological DBs, IR in Bioinformatics, search engines,ML Evaluation, search engine categories, EMRs, EHRs, Knowledge discovery, knowledge discovery techniques, Bayes’ theorem, Decision Tree, neural networks, Association rule, clustering, Machine learning, Ml applications, ML Other Applications, Data integration, Problems with data integration, Pattern Finding, Brute Force Algorithm, KMP Algorithm, KMP Prefix function, KMP Matcher, Boyer Moore Algorithm, Dot Plots, Scoring Scheme, Substitution Matrices, Optimal Algos, Needleman_wunch Algos, Needleman_wunch Execution, Smith_waterman Algo, PSA Complex Models, Computer Programs,  Programming languages, Java Introduction, anatomoy of Java Program,Introduction to Bio Java, Alphabets, Symbols and Sequences, Central Dogma,Sequence Input Output, Features and Annotations, Protein structure modules, Alignment Module, matlab introduction, Matlab Basics, BioInformatics Toolbox, features and functions, bioinformatics tasks, Phylogentic analysis, proteins and aas, Intoduction To Python, Python Basics, BioPython Basics, Intoduction To BioPython, SequenceObject, Phylogenetic tree IO, PHP part-1, PHP part-2, PHP part-3, Perl Basics, Unix/Linux Commands, Shell Scripting, Multiple Sequence Alignment, More on Multiple Sequence Alignment, Progressive Alignment for MSA, MSA Example, CLUSTAL, Structure Visualization - I, Structure Visualization - II, Experimental Determination of Protein Structure, Protein Data Bank, Visualization Techniques, Online Resources for Protein Visualization, Types of Protein Visualizations