Identify organism - Identify organism name from FASTA sequence (Nov/21/2009 )

Hi,
I am very new to bioinformatics field and so I am sorry if my question may sound very obvious.

I am looking for some guidelines how to solve my problem.
What I need is to write program which after reading FASTA file, containing many sequences (program should read both protein and DNA files), could identify organism names.
First, I am not sure how to perform this task directly, without writing any program, is it just performing BLAST and then selecting best matched sequence's organism name or there is some other method?
Second, how this should be performed in program, are there any web services to use or tools? I will be using bioJAVA.

Thanks

Maybe if my question was formulated somehow incorrect, or this task is unsolvable, I would appreciate it very much if you leave some comment.