Lecture 1

Lecture 2

Begining Perl

• Installing Perl
• Documentation
• Your first program
• Numbers and strings
• Literal
• Scalable variables
• Expressions and operators
• More operators
• Exercises

Blocs

• Conditions(if,else)
• Looping
• Other flux commands
• Receiving values in the command line (GetOpt)
• Exercises

Lecture 3

Lecture 4

Placing values in lists and arrays

• Returning elements in arrays
• Manipulating arrays
• Exercises
• Hashes
• Loading your Hash
• Returning data in a Hash
• Lists and Hashes
• Interesting Hash applications
• Exercises

Simple patterns

• Metacharacters
• Substitution
• Finding other patterns
• Exercises

Lecture 5

Lecture 6

Working with files

• Opening files
• Reading files
• Free files, testing files and binary data
• Exercises

Functions

• Creating and calling subroutines
• Scope
• Exercises
• Footnote function
• Exercises

Lecture 7

Lecture 8

CPAN

• Installing modules DBI and DBD::mysql
• Instanciating classes and using your methods
• Connecting to a database
• Insert
• Select
• Exercises

BioPerl

• Iniciation into BioPerl
• Installing BioPerl
• Documentation
• Reading FASTA files
• Counting the number of sequences in a file
• Counting the number of bases in a file
• Counting the number of bases ignoring certain characters
• Identifying motifs in a file
• Exercises

Lecture 9

Lecture 10

BioPerl - Reading annotation files (BenBank / EMBL)

• Counting the number of sequences in a file
• Counting the number of bases in a file
• Counting the number of bases ignoring certain characters
• Identifying motifs in a file
• Writing files
• Converting file formats
• Working with compacted files
• Exercises

BioPerl - Extracting sequences by ID

• Extracting and locating sequences by ID
• Reading Blast files
• Filtering Blast files
• Exercises