[Biojava-dev] Biojava 3 and intermolecular features

[Fabrice Jossinet]

Hi all,

When I used the previous releases of biojava, i had some problems to  
model inter-molecular features. For example interactions between two  
sequences/molecules in a tertiary structure or the interactions  
between two molecular partners in an interaction network. The feature  
should be the same, shared by (at least) 2 molecules but can be  
attached to different locations for each molecule.

With the current biojava model, a feature is composed of one location  
for a given sequence. Consequently, for the development of my previous  
software, I decided to change a little bit the biojava paradigm. For  
example, to model an intermolecular interaction between the region  
23-35 of mySeq1 and the region 34-46 of mySeq2 i have:

Feature myFeature = new InterMolecularInteraction();

mySeq1.addAnnotation(new Annotation(myFeature, new Location("23-35")));
mySeq2.addAnnotation(new Annotation(myFeature, new Location("34-46")));

The Annotation concept links a feature to a location and is attached  
to a sequence (this concept has no relation with the Annotation  
concept proposed by Biojava).

With this kind of model, I could also able to use the same concepts  
and strategy to model multiple alignments, which can also be seen as a  
kind of "inter-molecular relation".

Is there any plan to model these kind of features in biojava3? If no,  
can my proposal be a good start ?

Fabrice





--
Dr. Fabrice Jossinet
Laboratoire de Bioinformatique, modelisation et simulation des acides
nucleiques
Universite Louis Pasteur
Institut de biologie moleculaire et cellulaire du CNRS
UPR9002, Architecture et Reactivite de l'ARN
15 rue Rene Descartes
F-67084 Strasbourg Cedex
France

Tel + 33 (0) 3 88 417053
FAX + 33 (0) 3 88 60 22 18

f.jossinet at ibmc.u-strasbg.fr
fjossinet at gmail.com
http://www-ibmc.u-strasbg.fr/arn/Westhof/index.html
http://fjossinet.u-strasbg.fr/