BIOPERL TUTORIAL PDF

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BioPerl. An Introduction to Perl – by Seung-Yeop Lee; XS extension – by Sen Zhang; BioPerl .. [6] 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.

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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.

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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: