<div class="gmail_quote"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im"><br>
</div>UniprotFeature is currently only for sequence features annotated in<br>
Uniprot such as active sites, posttranslational modifications etc.<br>
These are parsed by my UniprotConnection class (using the uniprotjapi)<br>
and returned as UniprotFeatures. For Pdb structures associated with a<br>
Uniprot entry, I don't use the UniprotFeature class, but now thinking<br>
about it, it would also make sense to implement this as a feature.<br>
Instead, I'm using a very simple SiftsConnection class, which parses<br>
SIFTS (either locally or from the ftp site). The thing is that after<br>
taking the data from SIFTS (which gives you start and end residues in<br>
Uniprot and Pdb entry) you still need to do an alignment to get the<br>
actual residue mapping because there may still be gaps and/or<br>
mutations.<br></blockquote><div><br>Ok I didn't realise that, of course one would need both: uniprot annotation and pdb to uniprot mapping.<br><br><br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im"><br>
> - I'm not sure what the fields in the UniprotFeature are. What's the<br>
> uniprotTypeName and what's the description?<br>
<br>
</div>As mentioned, UniprotFeature stores sequence annotations as described<br>
in <a href="http://www.uniprot.org/manual/sequence_annotation" target="_blank">http://www.uniprot.org/manual/sequence_annotation</a>.<br>
uniprotTypeName is the category of annotation, e.g. Modified residue<br>
(actually the abbreviation returned by the uniprotjapi, i.e. MOD_RES)<br>
and description is the actual annotation, e.g. Phosphorylation.<br>
<div class="im"><br></div></blockquote><div><br>Cool thanks, I was thinking always in uniprot mapping so that's why I couldn't make any sense of this uniprotTypeName.<br><br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im">> - How do you go about storing the Collection of features belonging to a<br>
> certain structure/sequence. I can see that the HasFeatures interface intends<br>
> to help there. Have you already implemented something with it? That'd be<br>
> nice to have as an example.<br>
<br>
</div>I'm using a class 'Gene' which implements HasFeatures. I guess we<br>
could make the classes<br>
Pdb and/or Sequence to implement the HasFeatures interface as examples.<br>
For the moment, I'll send you my Gene class for reference.<br>
<div class="im"><br>
</div></blockquote></div><br>Yes that's tricky. The problem is that Pdb or Sequence could have more than one annotation attached to it, for instance Pdb can have uniprot annotation + catalytic sites annotation + structural domains +....... you name it. So how to use all of those together? If I understand it well the implementation of HasFeatures would only be for one type of Feature. Of course Pdb/Sequence could be subclassed case by case or something similar.... At some point we should really look for inspiration in other projects as Dan said :-)<br>
<br>Now I've just had new idea. Could one use generics for the HasFeatures interface and then implement several of them, something like HasFeatures<UniprotFeature>, HasFeatures<StructuralDomainFeature> and so on. Can one do that kind of thing?<br>
<br>Alright that's it for now<br><br>Nice weekend to all!<br><br>Jose<br><br>