[Bioperl-l] Locuslink?? Help

[Eric Wang]

Dear all,

I have on my hand a protein name and I want to access the locus link 
information and the NT_ contig information.
I tried several times with Bio::DB::GenBank objects but seems like I could 
only obtain the sequence but not the LL data.  So I guess my question is 
how would I go about finding the LocusLink information for this protein?

Thanks for all the help!!

Eric

 On Wed, 14 May 2003, Hilmar Lapp wrote:

> Are you talking about querying Genbank at NCBI through a 
> Bio::DB::GenPept object? I don't understand what exactly you're trying 
> to do. The LL parser in bioperl is a stream parser, not a random access 
> interface.
> 
> My recommendation is to state what you are trying to achieve, paste in 
> the script or the part that supposedly does this, and send that to the 
> list. There's many more very knowledgeable people there ... who may 
> have even tried to do the same as you before.
> 
> 	-hilmar
> 
> On Wednesday, May 14, 2003, at 10:46  PM, Eric Wang wrote:
> 
> > Thanks for your help.
> > I am still confused on how to query locuslink for the tags
> > I have on my hand just the protein name and I want to basically find 
> > the
> > intron/exon boundaries.
> > But it seems like when I use get_stream_by_query('prot_name'), I got
> > nothing... do you know a better way to approaching the problem?
> >
> > Thanks
> > Eric
> >
> > On Wed, 14 May 2003, Hilmar Lapp wrote:
> >
> >> Theoretically yes, but be aware that these might be huge. If you fetch
> >> them remotely, you don't do a favor to anyone, not to NCBI and not to
> >> yourself. You want to have a local indexed flat file download for 
> >> that.
> >>
> >> 	-hilmar
> >>
> >> On Wednesday, May 14, 2003, at 08:40  PM, Eric Wang wrote:
> >>
> >>> Thanks for your help!
> >>> Yeah, I noticed there isn't any top_features but
> >>> the annotations will contain reference sequence (NT_ contigs) ?
> >>> if that's the case, I would just use get_seq_by_id to retrieve it
> >>> right?
> >>>
> >>>
> >>>
> >>> Thanks again
> >>>
> >>> Eric
> >>> On Wed, 14 May 2003, Hilmar Lapp wrote:
> >>>
> >>>> my $seqio = Bio::SeqIO->new(-format => "locuslink");
> >>>> while(my $ll = $seqio->next_seq()) {
> >>>> 	# whatever
> >>>> }
> >>>>
> >>>> There won't be any sequence features though. LL essentially is lots 
> >>>> of
> >>>> tag/value pairs, and that is how it ends up (i.e.,
> >>>> $ll->annotation->get_Annotations()).
> >>>>
> >>>> The locus-contains-splice variants thing in LL isn't properly
> >>>> reflected
> >>>> in the resulting SeqI object, which is a problem of the Bioperl 
> >>>> object
> >>>> model in the first place (there is no good object right now that 
> >>>> would
> >>>> properly reflect an LL object wrt the datatype). What you'd want is 
> >>>> a
> >>>> gene model. Maybe it's worth thinking whether the feature-driven
> >>>> SeqFeature::Gene::* objects fit the bill here. I'm not convinced yet
> >>>> though.
> >>>>
> >>>> 	-hilmar
> >>>>
> >>>> On Wednesday, May 14, 2003, at 05:44  PM, Eric Wang wrote:
> >>>>
> >>>>> I have a question regarding how to retrieve locuslink objects.
> >>>>> I searched the documentation everywhere and couldn't find it.
> >>>>> Can anybody give me some pointers on how to retrieve locuslink
> >>>>> objects
> >>>>> and
> >>>>> can I use the top_Seqfeatures() for this object?
> >>>>>
> >>>>> Thanks in advance
> >>>>>
> >>>>> Eric
> >>>>>
> >>>>> _______________________________________________
> >>>>> Bioperl-l mailing list
> >>>>> Bioperl-l at bioperl.org
> >>>>> http://pw600a.bioperl.org/mailman/listinfo/bioperl-l
> >>>>>
> >>>>
> >>>
> >>>
> >>
> >
> >
>