[Biojava-l] hello

[Thomas Down]

>   I have a question about biojava. 
>   If I have some information about annotation of a genome, can I
> output them with a ASN.1 format through biojava? The format ASN.1
> is used to submit annotated sequence to Genbank. Does biojava have
> the function to generate this kind of files automatically if these
> annotation have been read in java program?

Hello!

Unfortunately, BioJava doesn't currently have any code for
handling Genbank ASN.1 -- only Genbank flatfiles.  I hadn't
realized that Genbank required submission in ASN.1.  It sounds
like this would be a good feature to support -- Greg Cox (who
has done a lot of work on our Genbank flatfile support) might
have something to say about this.

Of course, another possibility is to submit sequences to
EMBL (which does accept flatfiles, and which synchronizes
nightly with Genbank).

Or is there a Genbank flatfile -> ASN.1 conversion utility
out there somewhere?

    Thomas.