Hi,
Happy New Year 2012!
Having read the public Galaxy server now has ENA/SRA data available I'm wondering if EBI's dbfetch or wsdbfetch is an option to consider as well. Dbfetch has a web interface and is also supported using Web Services:
Web: http://www.ebi.ac.uk/Tools/dbfetch/ and WS: http://www.ebi.ac.uk/Tools/webservices/services/dbfetch (both SOAP and REST are supported). The REST interface is available from: http://www.ebi.ac.uk/Tools/webservices/services/dbfetch_rest
Briefly, dbfetch provides access to 47 datasets. These include mainstream nucleotide (EMBL-Bank, ENA/* & RefSeq) and protein sequence databases (UniProt and UniParc), ENSEMBL, ENSEMBL Genomes, PUBMED/MEDLINE, PDBe, etc. It returns entries and documents in flatfile, raw, hypertext, fasta and current XML formats.
Yours sincerely,
Rodrigo Lopez EMBL-EBI/ES