[Biojava-l] what it needs to do this with (Bio)Java...

[Gerald Loeffler]

Hi!

I have a few (really simple) sequence analysis steps to perform for a
project of mine, would like to do this in pure Java, but can't quite
judge whether the code available in BioJava right now is up to the task.
So - I'd be very grateful for a short reply of yours that would give me
some insight into whether the following tasks are

	_now_ _really_ possible with BioJava

(or any other pure Java implementation, for that matter), a few

	brief hints on how to actually do this with BioJava

or - alternatively - some guidance on

	what I would need to add to BioJava

in order to be able to do what I want to do. The simple tasks I'd like
to do are:

	o given a Java String object that contains a nucleotide sequence,
construct a "NT-Sequence" object
	o given a file of FASTA-formatted nt-sequences, instantiate a
Collection of "NT-Sequence" objects
	o given 2 "NT-Sequence" objects, construct the optimal alignment
between them, return it as an "Alignment" object, and also give a Score
for the alignment. (I know, this is gonna be slow, but it's fine for my
application...)
	o given an "Annotated NT-Sequence" object, write a GenBank-file
containing both sequence and annotation (features)
	o given an "NT-Sequence" object, construct its reverse complement
"NT-Sequence" object
	o given an "NT-Sequence" object, construct its translated "AA-Sequence"
object.

Thanks for your time!!

	cheers,
	gerald
-- 
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