PI-670: Pharmacoinformatics - Perl Programming		(1 credit)
1.	Introduction to Perl: History, Applications, Built in functions, Data types, introduction to operators, print function, command line program, user input using operator, Perl and operating systems, Shebang Directive.
2.	Perl operators: Arithmetic operators, Relational operators, Logical operators – And, Or, Not, assignment operator, Bitwise operators, precedence of operators, auto increment and decrement operators, chomp, comma operators and usage, placing increment operators before and after variable, significance.
3.	Scalar variable: Identifier, Special characters in scalar variable names, Assignment of scalar variable, Strings and Numbers, Single quoted and Double quoted strings, back slash interpretation, variable interpolation, scalar variable in number and string context
4.	Regular arrays and Hash arrays: Identifiers, Creating arrays, Accessing and retrieval of elements, Array slices, Array operators- Push & Pop, Unshift & Shift, Hash arrays, Keys, Values, Retrieval of elements.
5.	Control structures: Statement blocks, Branching structures, if/else, nested if/else statements, Looping Structures, The while statement, The until statement, do…while and do…until structures, The for loop, initial expression, test expression, increment expression, Variations of the for loops, for loops as timing mechanisms for programs, foreach loop, for loops and operators, Perl programs using control structures.
6.	Subroutines: Subroutine data types, Declaring subroutines, Calling subroutines in Perl, Writing subroutine, Return function, Scope of variables in subroutines, Global variables, Local variables-dynamics and lexical variable, Advantage and disadvantages of variables, Returning value from subroutines, Examples using Perl programs.
7.	File handles: Standard input and Standard output, Formatted output, printf functions, printf for character, decimal and floating point numbers, Angle operators, Here strings, Here as markers, Printing with here strings, File input/output, Opening and closing files, reading, writing, appending, File tests, Handling file opening errors, warn and die functions, File tests, Examples using Perl programs.
8.	Pattern matching and Regular expressions: Special character for pattern matching, Writing regular expressions, Meta characters for beginning and ending of strings, Special variables, Wild cards, Quantifiers, Matching specific types of characters- single digit, single word, white space character, Invert digits, words, white space, invert character classes, Flags for case insensitive, Sub expressions, Examples using Perl programs.
9.	Biocomputing: Introduction to BioPerl, Retrieval. Installing Procedures, Architectures, General BioPerl Classes, Sequences -Bio::Seq, Bio::SeqIO, Bio::Align class etc, Sequence Manipulation, Features and Location Classes-Extracting CDS, Alignments -AlignIO, Analysis -Blast, Databases- Database Classes, Accessing a Local Database alignment of sequences using applications