[Biojava-l] How to - Collection of features only?

[mark.schreiber at novartis.com]

Hi -

You can use a dummy sequence as the anchor for your sequences.
org.biojava.bio.seq.SequenceTools.createDummy()

- Mark






czaleski at albany.edu
Sent by: biojava-l-bounces at lists.open-bio.org
08/08/2006 12:33 AM
Please respond to czaleski

 
        To:     biojava-l at biojava.org
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] How to - Collection of features only?


Greetings,

I have a question about coordinate-only data. I have a database with many
flavors of annotation, and I build collections of objects from this data
(usually Sequences). However I have an instance where I need to retrieve
coordinate based data only. For instance, I'd fetch something like all 3'
UTRs  defined in my RefSeq table, and then build a .bed file to be loaded
into UCSC's genome browser. In this case, I need the coordinates only
(chromosome, txStart, txEnd) and I do not need the actual sequence.

So basically I'd like to make a collection of Features. But since in the
tutorial is says: "Features cannot be created independently of a
sequence", how would I do this? I expect I could create a Sequence object
with an empty or null String/SymbolList, and then add a single Feature to
each... but this does not seem like it would be the intended solution.

Is there some other method by which I could/should accomplish this?

Thanks very much
Chris
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