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 software 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 software program, are there any web services to use or tools? I will be using bioJAVA.