| 18th January 2021 08:53 AM | |
| Arvind Kumar | Sathyabama Institute of Science and Technology B.Tech - BioTechnology SBTA3008 PERL for Bioinformatics Syllabus Sathyabama Institute of Science and Technology B.Tech - BioTechnology SBTA3008 PERL for Bioinformatics Syllabus SATHYABAMA INSTITUTE OF SCIENCE AND TECHNOLOGY SCHOOL OF BIO AND CHEMICAL ENGINEERING SBTA3008 PERL FOR BIOINFORMATICS L T P Credits Total Marks 3 0 0 3 100 UNIT 1 INTRODUCTION 9 Hrs. Biology and Computer Science - Limits to Computation - Getting Started with Perl - Perl's Benefits - Installing Perl on Your Computer - Running Perl Programs on various platforms - The Art of Programming - An Environment of Programs - Programming Strategies - The Programming Process - Sequences and Strings - Representing Sequence Data - A Program to Store a DNA Sequence - Control Flow - Comments Revisited - Command Interpretation – Statements – Variables – Strings UNIT 2 STARTING TO CODE AND GETTING HELP 9 Hrs. Concatenating DNA Fragments - Transcription: DNA to RNA - Using the Perl Documentation - Calculating the Reverse Complement in Perl - Proteins, Files, and Arrays - Reading Proteins in Files – Arrays - scalar and List Context - Motifs and Loops - Flow Control - Conditional Statements - open and unless UNIT 3 WRITING MORE CODE 9 Hrs. Finding Motifs - Regular Expressions - Counting Nucleotides - Exploding Strings into Arrays - Operating on Strings - Writing to Files - Subroutines and Bugs - Subroutines - Scoping and Subroutines - Command-Line Arguments and Arrays - Passing Data to Subroutines - Modules and Libraries of Subroutines - Fixing Bugs in Your Code - The Perl Debugger UNIT 4 MANIPULATING MACROMOLECULES AND DATABASES 9 Hrs. Mutations and Randomization - A Program Using Randomization - A Program to Simulate DNA Mutation - Generating Random DNA - Analyzing DNA - The Genetic Code – Hashes - Data Structures and Algorithms for Biology - A Gene Expression Database - Gene Expression Data Using Unsorted Arrays - Gene Expression Data Using Hashes - Relational Databases - Translating Codons to Amino Acids - Translating DNA into Proteins - Reading DNA from Files in FASTA Format - Reading Frames - Translating Reading Frames UNIT 5 RESTRICTION MAPS, REGULAR EXPRESSIONS AND MORE 9 Hrs. Regular Expressions - Restriction Enzyme Data - Logical Operators and the Range Operator - Finding the Restriction Sites - Perl Operations–GenBank - GenBank Files - Libraries - Separating Sequence and Annotation - Parsing Annotations- When to Use Regular Expressions - Protein Data Bank – Recursion - PDB Files - PDB File Format - Parsing PDB Files – BLAST - String Matching and Homology - BLAST Output Files - Parsing BLAST Output - Extracting Annotation and Alignments - Parsing BLAST Alignments - The printf Function – Bioperl - Bioperl Tutorial Script Max. 45 Hrs. TEXT / REFERENCE BOOKS 1. James Tisdall. Mastering Perl for Bioinformatics. O'Reilly Media, 2010. 2. Michalski, Brent, et al. Beginning Perl, John Wiley & Sons, Incorporated, 2012. 3. Dwyer, Rex A. Genomic Perl, From Bioinformatics Basics to Working Code, Cambridge University Press, 2002. 4. Holzner, Steven. Perl Black Book, Paraglyph Press, 2001. 5. Dominus, Mark Jason, Higher-Order Perl: Transforming Programs with Programs, Elsevier Science & Technology, 2005. 6. Oualline, Steve. Wicked Cool Perl Scripts: Useful Perl Scripts That Solve Difficult Problems, No Starch Press, Incorporated, 2006. 7. Krumins, Peteris. Perl One-Liners: 130 Programs That Get Things Done, No Starch Press, Incorporated, 2013. END SEMESTER EXAMINATION QUESTION PAPER PATTERN Max. Marks: 100 Exam Duration: 3 Hrs. Part A: 10 Questions of 2 marks each - No choice 20 Marks Part B: 2 Questions from each unit of internal choice, each carrying 16 marks 80 Marks |
