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Bioinformatica 10-11-2011-p6-bioperl

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Prof. Wim Van Criekinge
Prof. Wim Van Criekinge

The document discusses BioPerl, an open source collection of Perl modules for bioinformatics tasks. It provides examples of using BioPerl to work with sequence objects, read sequences from files in different formats, and retrieve sequences from GenBank. Methods are demonstrated for looping through sequences, converting file formats, and calculating properties like isoelectric points. The most acidic and basic amino acids can be identified by isoelectric point, and there is a biological explanation for these results.

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FBW 10-11-2011 Wim Van Criekinge
Three Basic Data Types ,[object Object],[object Object],[object Object]
[object Object],[object Object],[object Object]
The ‘structure’ of a Hash ,[object Object],[object Object],[object Object],Index Value Key (name) Value ,[object Object]
[object Object],[object Object],[object Object],Sub routine
Overview ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Multi-line parsing ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Advanced data structures in Perl ,[object Object],[object Object]
References: Scalars ,[object Object],[object Object],[object Object],[object Object],[object Object]
Reference to arrays ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
References to hashes ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Anonymous References ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Anonymous …
Programming paradigms ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
The key idea ,[object Object],[object Object],[object Object]
Perl 00 ,[object Object],[object Object],[object Object]
Perl Classes ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Bioperl.pl ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
.. /site/lib/bio/Sequentie.pm ,[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]
Bless ,[object Object]
Bioperl.pl ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Bless ,[object Object],[object Object]
Method: NEW (constructor) ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Random Sequence an OO Way ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Review ,[object Object],[object Object],[object Object],[object Object],[object Object]
CPAN ,[object Object]
What is BioPerl? ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
What BioPerl isn’t ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Installing Modules ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Bioperl installation ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Installation on Windows (ActiveState) ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Directory Structure ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
 
[object Object],[object Object],[object Object]
Sequence Object Creation ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Multi-line parsing ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Live.pl ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Live2.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]
File converter ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Changing Formats (with Filehandles): ,[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]
 
Oef 1 ,[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]
Oef 2 ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
So what is BioPerl? (continued…) ,[object Object],[object Object],[object Object],[object Object],[object Object]
Searching for Sequence Similarity ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Remote Execution of BLAST ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Example of Remote Blast ,[object Object],[object Object],[object Object],[object Object],[object Object]
Example ,[object Object],[object Object],[object Object],[object Object],[object Object]
Parsing BLAST and FASTA Reports ,[object Object],[object Object],[object Object],[object Object],[object Object]
Parsing Blast Reports ,[object Object],[object Object],[object Object],[object Object]
Sample Script to Read and Parse BLAST Report ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Parsing BLAST Using BPlite, BPpsilite, and BPbl2seq ,[object Object],[object Object],[object Object],[object Object],[object Object]
Parse BLAST output ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Parse BLAST in a little more detail ,[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]
SearchIO parsers: ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
What else is in BioPerl? ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Some advanced BioPerl ,[object Object],[object Object],[object Object]
Some really advanced BioPerl ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
GBrowse (Generic Genome Browser)

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