MTech Perl Programming And Bioinformatics syllabus for 2 Sem 2020 scheme 20BBI254

Introduction to Perl, Downloading and installation from Website, Writing and Running a Perl Program, Editing, Advantages Data Types: Scalar data and scalar variables: Number, String, Conversion between Numbers and Strings, Variable Interpolation, Arithmetic and Decimal Precision, Arrays: Initialization, Manipulation of Array elements; Associative Array (Hashes): Initialization, Manipulation of Elements of Array.

Arithmetic and Logical Operators:

Arithmetic Operators, Assignment Operators, Increment and Decrement Operators, String Concatenation and Repetition, Operators precedence and Associativity, Conditional Operators, Logical Operators, Operators for manipulating arrays, Operators for Manipulating hashes.

Conditionals and Loops:

Conditional Statement; if, if…else, if and if-else, unless statement, Loops: while, for, until, do..while, do..until and foreach loop, last next, redo, continue and case switch statement. Input and Output: Creating a file, Reading Data from a file, Writing data to a file, Closing a file, Managing Files and Directories.

Regular Expressions and Pattern Matching:

Regular Expression, Pattern Matching, Meta Character, Simple Pattern, Matching Group of Characters, Matching multiple instances of Characters, Pattern Building, Pattern and Variable, Pattern and Loops, Using Pattern for Search and Replace, Matching Pattern over multiple Lines etc.

Built-in Functions, Defining and calling subroutines, Returning Values from Subroutines, Using Local Variables in Subroutines, Passing Values into Subroutine, Perl References, Perl module and their uses.

Applications of Perl in Bioinformatics:

Concatenating DNA Fragments, Transcription: DNA to RNA, Reading Protein Files, Finding Motifs, Simulating DNA, Generating Random DNA, Analysing DNA, Translating DNA to Proteins, Reading DNA from Files in FASTA format, Separating Sequence and Annotation, Parsing Annotation, Parsing PDB files, Parsing BLAST output, Bio-perl .

Course outcomes:

At the end of the course the student will be able to:

• learn the basics of Perl syntax, functions and algorithms used in coding
• Understand the applications of perl programming for various bioinformatics exercises.

Question paper pattern:

The SEE question paper will be set for 100 marks and the marks scored will be proportionately reduced to 60.

• The question paper will have ten full questions carrying equal marks.
• Each full question is for 20 marks.
• There will be two full questions (with a maximum of four sub questions) from each module.
• Each full question will have sub question covering all the topics under a module.
• The students will have to answer five full questions, selecting one full question from each module.

Textbook/ Textbooks

1 Perl Programming for Biologists D. Curtis Jamison Wiley-IEEE 2003

2 Mastering Perl for Bioinformatics James T Tisdall  O'Reilly Media, Inc, USA 2007

Reference Books

1 Beginning Perl for Bioinformatics James T Tisdall O’Reilly & Associates 2001

2 Building Bioinformatics Solutions: With Perl Conrad Bessant, Darren Oakley, Ian Shadforth Oxford 2010

3 Genomic Perl: From Bioinformatics Basics to Working Code Rex A. Dwyer Cambridge University Press 2002