BIOPERL TUTORIAL PDF
BioPerl. An Introduction to Perl – by Seung-Yeop Lee; XS extension – by Sen Zhang; BioPerl ..  and It will cover both learning Perl and bioperl. have an advice for you If you are totally beginner and you just want to learn any programming. Bioperl is a collection of more than Perl modules for bioinformatics that have installing it, and exploring the tutorial and example material that it provides.
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BioperlOverview Bioperl Overview http: A collection of Perl modules for processing data for the life sciences A project made up of biologists, bioinformaticians, computer scientists An open source toolkit of building blocks nioperl life sciences applications Supported by Open Bioinformatics Foundation O B Fhttp: In perl strings, arrays, etc start with 0.
When using a module, CaseMatTers. Make sure you know what you’re getting back – if you get back an array, don’t assign it to a scalar in haste.
Here if bioperl is installed using script Publication – Stajich et al. Genome Res Bioperl mailing list: Methods can be overridden by children Interfaces Interfaces can be thought of as an agreement Object will at least look a certain way It is independent of what goes on under the hood Interfaces and Inheritance in Bioperl What you need to know: Interfaces are declared with trailing ‘I’ Bio:: PrimarySeqI Can be assured that at least these methods will be implemented by subclasses Can treat all inheriting objects as if they were the same, i.
Bioperl Tutorial | h Kumar –
RichSeq all have basic Bio:: In Perl, good OO requires good manners. Methods which start with an underscore are considered ‘private’ Watch out.
boiperl Perl programmers can cheat. Examples of modular programming From Stein et al. PrimarySeq – Basic sequence operations aa and nt Bio:: Seq – Supports attached features Bio:: LocatableSeq – subsequences Bio:: Generic – Basic Sequence features Bio:: Similarity – Represent similarity info Bio:: XX objects Class diagram subset From Stajich et al.
Genome Research Build a sequence and translate it!
Seq Initialization annotation – Bio:: AnnotationCollectionI object features – array ref of Bio:: SeqFeatureI objects species – Bio:: Fruit fly Drosophila melanogaster Hart A. SeqIO Can read sequence from a file or a filehandle special trick to read from a string: LocationI, and implementations in Bio:: Bbioperl – multiple locations join,order Bio:: Create a sequence and a feature use Bio:: XX Local databases local Iboperl – Bio:: XX local alignments – Bio:: BioSeqDatabases through bioperl-db pkg Retrieve sequences from a database ex6.
BioPerl Tutorial: Extracting DNA Sequences From a Database – eXtension
Index biosql biofetch – Bio:: SearchIO – Parser Bio:: XX – Data Objects Bio:: AlignIO – Parser Bio:: Blast Deprecated – Bio:: Components of the Hit which match the query. Corresponding object types tuhorial the Bio:: Biblio – Bibliographic objects Bio:: CodonTable – represent codon tables Bio:: SeqStats – base-pair freq, dicodon freq, etc Bio:: SeqWords – count n-mer words in a sequence Bio:: RestrictionEnzyme – find restriction enzyme sites and cut sequence Bio:: Consed – process Consed data Bio:: Tree – Phylogenetic Trees Nioperl Map – genetic, linkage maps rudiments Bio:: Tutorila – transformations between coordinate systems Bioperl can help you run things too Namespace is Bio:: Run In separate CVS module bioperl-run since v1.
Some people who really got the project started and kept it going: