Users of my lab use a java webapp to save their sequences of staph aureus 16S coming from hospital patients. When they submit a sequence into the database, I would like to save the information of the submit page into a genbank file but I don't know to proceed without use of biojava.
NCBI provides two software packages, of which I am aware, for this purpose. One is Sequin and the other is BankIt. Under Data and Software, see the page for submissions for links to these and other submission tools. You could use these tools to create GenBank-styled entries for local use. You would not have to submit the data to NCBI but it would be in a format comparable to those entries already in the NCBI databases.
Are you wanting to create a "flat file" version of the sequence, or a GenBank ASN.1 version? Either way, the simplest way to get there is probably to use NCBI's
tbl2asn tool, which will convert FASTA sequences to ASN.1. If you want the flat file, you can then use
Download location: ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/cmdline/