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