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

czaleski at albany.edu czaleski at albany.edu
Mon Aug 7 16:33:52 UTC 2006


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

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