Perl for Bioinformatics

Introduction to Bioinformatics
Introduction to Perl

Perl
Scalar Data

101	Numbers
102	Strings, 5-5,
103	Double-quoted strings
104	Single-quoted strings, 4-1, 4-2,
105	Scalar operators
106	Operators for numbers
107	Operators for numbers-cont
108	Operators for strings
109	Program protocol.pl
110	Reading data from Standard Input
111	The chop and chomp function
112	Summary

Built in Functions

Arrays

401	Definition and syntax
402	The foreach construct
403	A slight diversion - binary assignment operators
404	Examples for using the foreach construct - cont.
405	Printing all array elements at once, 4-8,
406	Accessing individual array elements
407	Accessing a group of elements from an array
	Assignment of a list into an array slice
	Assignment of an array (or list) into another array
408	Summary of main concepts until now
409	Array content: examples
410	The sort function
411	The push and shift functions
412	What will happen if...
413	Length of a given array
414	Summary

Array Functions

Functions

301	Syntax
302	Arguments, return value and the my operator, 6-1,
303	Global vs. Private Variables in Functions
304	More on Passing Arguments to a Function
305	More on Capturing Arguments in a Function
306	Functions can be called without arguments

Writing Safe Code

001	Declare your variables with my
002	Examples for the effect of my in loops
003	Examples for the effect of my in functions, 6-2,
004	An example program using my (I)
005	An example program using my (II)
006	Enforcing the usage of my by the strict module
007	Using the warnings module or the -w switch
008	Using the diagnostics module

Control Structures

701	Introduction
702	The if and unless statements, 5-1, 5-2, 5-3,
703	Variations on the if statement
704	What is truth?
705	The while and until loops
706	Comparison operators
707	The do {} while / until loop
708	The foreach loop
709	The for loop
710	Summary

File Input/Output

801	Redirection of output to a file
802	Filehandles
803	Opening a filehandle
804	Closing a filehandle, 4-5, 4-6, 4-7,
805	The die function
806	Using filehandles for writing
807	Using filehandles for reading
808	Examples, 5-6,
809	The printf function
810	Filehandles and Buffers

Basic Text Processing

901	The substr function
902	Examples for using the substr function, 8-1,
903	The split function
904	Example for using the split function
905	The join function

Hashes, Loop Control

b01	Definition and syntax
b02	Examples
b03	Assignment into a hash variable
b04	Accessing individual hash elements
b05	Adding and deleting elements to/from a hash
	Checking whether a hash is empty.
b06	The keys function
b07	The values function
b08	Iterating over all elements of a hash using the each function
b09	Iterating over all hash elements: When should I use the keys and when the each function?
a01	The loop control statements
a02	An example for using the last command
a03	An example for using the next command
a04	An example for using the redo command

Data Base Management, Sorting

b02	Opening and Closing DBM Hashes
b03	Using a DBM Hash
b04	Storing multiple fields under one key
c01	Sorting array elements
c02	Sorting a hash by value

Regular Expressions

d01	Definitions and uses
d02	Match to a sequence of characters
d03	Match to a character class
d04	Predefined character classes
d05	Quantifiers
d06	The dot special character
d07	Case-insensitive pattern matching
d08	Alternation
d09	Anchoring a pattern to the beginning or end of a string
d10	Parenthesis as memory
d11	Greediness and laziness
d12	Parenthesis as memory - notes
d13	Substitutions, 5-4, 5-7,
d14	Variable interpolation
	Meta-characters

6-3	6-4	7-1	7-2	7-3
7-4	8-2	8-3

Assignments

Server	Internet	WWW
Browser	HTML	HTML HP

CGI Programming

e01	Introduction
e02	Creating a static HTML file by a Perl program
e03	Creating a Web page "on the fly" by a CGI-program
e04	Guidelines for HTML page generation by a CGI-program
e05	Receiving CGI-program arguments from the URL
e06	Receiving CGI-program arguments from the URL (cont)
e07	Using CGI.pm for parsing the query string
e08	Receiving CGI-program arguments from a Web form
e09	HTML forms
e10	Form Example
e11	Read more about CGI.pm
e12	When should I use the URL and when a Web form for passing arguments to a CGI-program?
e13	Querying a Web-based database - an example
e14	Handling error messages
	CGI.pm - a Perl5 CGI Libray

Process Management
References and Data Structures

Bioinformatics
Public Databases Data Formats
Sequence Alignment and Searching
Gene Prediction
Multiple Sequence Alignment
Phylogenetic Analysis
Patterns and Profiles from Sequence Data
Protein Sequence Analysis
Protein Structure Prediction
Protein Structure Property Analysis
Protein Structure Alignment and Comparison
Predicting Structure & Function from Sequence
Tools for Genomics and Proteomics

References:

Perl Programming Course for Bioinformatics and Internet .... Dr Jaime Prilusky

Beginning Perl for Bioinformatics   By James Tisdall

Developing Bioinformatics Computer Skills  By Cynthia Gibas, Per Jambeck

Mastering Perl for Bioinformatics By James Tisdall

Introduction to Bioinformatics By Arthur M. Lesk

Learning Perl, Second Edition
Randal L. Schwartz and Tom Christiansen, O'Reilly & Associates, Inc., Sebastpool, CA (1997).
Programming Perl, Second Edition
Larry Wall, Tom Christiansen and Randal L. Schwartz, O'Reilly & Associates, Inc., Sebastpool, CA (1996).
Official Guide to Programming with CGI.pm
Lincoln Stein, John Wiley & Sons, Inc. (1998).