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Bioinformatica 06-10-2011-p2 introduction

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Prof. Wim Van Criekinge
Prof. Wim Van Criekinge

The document discusses topics related to practicing bioinformatics including: - Installing and working with the TextPad text editor - Regular expressions (regex), including patterns, quantifiers, anchors, grouping, alternation, and variable interpolation - Using regex memory variables ($1, $2, etc.) to extract matched substrings - The s/// substitution operator and tr/// translation operator - Applying these skills to tasks like finding restriction enzyme cut sites in DNA sequences

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FBW 06-10-2011 Wim Van Criekinge
Practicum Bioinformatica ,[object Object],[object Object],[object Object],[object Object],[object Object]
Programming ,[object Object],[object Object],[object Object],[object Object],[object Object]
Three Basic Data Types ,[object Object],[object Object],[object Object]
Customize textpad part 1: Create Document Class
[object Object]
Customize textpad part 2: Add Perl to “Tools Menu”
[object Object],[object Object],[object Object],[object Object],[object Object]
Unzip to textpad samples directory
Bereken Pi aan de hand van twee random getallen 1 x y
[object Object],[object Object],[object Object],[object Object]
[object Object]
Two brief diversions (warnings & strict) ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Practicum Bioinformatica ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
What is a regular expression? ,[object Object],[object Object],[object Object]
Why would you use a regex? ,[object Object],[object Object],[object Object],[object Object],[object Object]
Regular Expressions ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
[object Object],[object Object],[object Object]
Regular Expressions ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Constructing a Regex ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Looking for a pattern ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Regular Expression Atoms ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
More atoms ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
An example ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Quantifiers ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Anchors ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Grouping ,[object Object],[object Object],[object Object],[object Object]
Alternation ,[object Object],[object Object],[object Object]
Variable interpolation ,[object Object],[object Object],[object Object],[object Object],[object Object]
Regular Expression Review ,[object Object],[object Object],[object Object],[object Object]
Remembering Stuff ,[object Object],[object Object],[object Object],[object Object],[object Object]
Memory Parentheses (pattern memory) ,[object Object],[object Object],[object Object],[object Object]
Getting at pattern memory ,[object Object],[object Object],[object Object],[object Object],[object Object]
An example of pattern memory ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Finding all instances of a match ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Perl is Greedy ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Substitute function ,[object Object],[object Object],[object Object],[object Object],[object Object]
Using s ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Substitutions
tr function ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Translations
Using tr ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
[object Object],[object Object],[object Object],[object Object],[object Object]
[object Object],[object Object],[object Object]
Regex ,[object Object],[object Object],[object Object]
Oefeningen practicum 2 ,[object Object],[object Object],[object Object],[object Object],http://us.expasy.org/prosite/                         
[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
 
Three Basic Data Types ,[object Object],[object Object],[object Object]
Arrays ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
The foreach construct ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Examples for using the foreach construct - cont. ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Accessing individual array elements ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
The sort function ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
The push and shift functions ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
How can I know the length of a given array? ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Special array for command line arguments @ARGV ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Perl Array review ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Generate random string ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Text Processing Functions ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Text Processing Functions ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Three Basic Data Types ,[object Object],[object Object],[object Object]
When is an array not good enough? ,[object Object],[object Object],[object Object],[object Object]
Problem solved: The associative array ,[object Object],[object Object],[object Object],[object Object],[object Object]
The ‘structure’ of a Hash ,[object Object],[object Object],Index Value
The ‘structure’ of a Hash ,[object Object],[object Object],[object Object],Index Value Key (name) Value ,[object Object]
Hash Rules: ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Creating a hash ,[object Object],[object Object],[object Object],[object Object],[object Object]
Getting at values ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Getting at values, continued ,[object Object],[object Object],[object Object]
A phone book program ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Count unique things with a hash
Printing a Hash ,[object Object],[object Object],[object Object],[object Object]
[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Printing a hash (continued)
[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Programming in general and Perl in particular
[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Programming in general and Perl in particular
[object Object],[object Object],Oefeningen practicum 2
[object Object],[object Object]
[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],'AUU','I', 'AUC','I', 'AUA','I', 'AUG','M', 'ACU','T', 'ACC','T', 'ACA','T', 'ACG','T', 'AAU','N', 'AAC','N', 'AAA','K', 'AAG','K', 'AGU','S', 'AGC','S', 'AGA','R', 'AGG','R', 'GUU','V', 'GUC','V', 'GUA','V', 'GUG','V', 'GCU','A', 'GCC','A', 'GCA','A', 'GCG','A', 'GAU','D', 'GAC','D', 'GAA','E', 'GAG','E', 'GGU','G', 'GGC','G', 'GGA','G', 'GGG','G' );
[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
 
 
 
Palin.fasta ,[object Object],[object Object]
Palingram.pl ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],print "Set van palingram"; while(($key, $value) = each (%palhash)) { print "$key => $value"; }

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