[Bioperl-l] Protein interaction modules

[Brian Osborne]

Chris,

It looks like these 2 modules should be added to Bioperl::Bundle:

Class::AutoClass
Clone


Brian O.


-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Richard Adams
Sent: Thursday, July 15, 2004 5:55 AM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] Protein interaction modules

Hello BioPerlers,
I'd like to bring to peoples' attention some modules for parsing and
analyzing protein interaction data.
They are in CVS under Bio/Graph and are :

Bio/Graph/IO
Bio/Graph/IO/dip
Bio/Graph/IO/psi_xml

are modules for reading /writing graph data and function in an analagous
way to the SeqIO system.

Bio/Graph/SimpleGraph
Bio/Graph/SimpleGraph/traversal

are generic graph modules written by Nat Goodman and provide
functionality for traversing and building graphs.
These are independent of BioPerl but are added here as they're not in
CPAN yet.

Bio/Graph/ProteinGraph
Bio/Graph/Edge

extend the SimpleGraph modules to deal with multiple sequence
identifiers, duplicate edges  and more complex
data about the nature of an interaction.

In this implementation, nodes are Bio::Seq objects. Interactions are
represented by Bio/Graph/Edge objects


These modules are very much biologically orientated,  and are written
with the following sort of tasks in mind:

E.g.,

How can I annotate my sequences with interaction data?
Which nodes cause the most disruption to the network if perturbed?
What happens to network properties if a node is deleted?
How can I merge 2 protein interaction data sets together, and find
duplicate interactions?
How can I calculate basic graph properties of my interaction data set ?
    e.g., density, clustering coefficient.

 code to demonstrate some of these tasks can be found in the Synopsis of
Bio/Graph/ProteinGraph.
There is test suite , t/protgraph.t which test most of the methods.

I'd be very interested in feedback, ideas for what to include in a
protein/DNA or protein/RNA interaction class,
bugs etc.

To use these modules you need:
XML::Twig if you want to parse XML
Clone
Class::AutoClass - the SimpleGraph modules depend on this.
The test suite tests for these modules.

Obvious improvements are :

AT present the XML parser just gets the basic interaction data, not the
full dataset.
An psi_xml writer.

Richard

--
Dr Richard Adams
Psychiatric Genetics Group,
Medical Genetics,
Molecular Medicine Centre,
Western General Hospital,
Crewe Rd West,
Edinburgh UK
EH4 2XU

Tel: 44 131 651 1084
richard.adams at ed.ac.uk


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