8.9 years ago by
Most online BLAST servers do not permit batch BLAST. It's unfortunate that whilst the Greengenes server is an exception to this, it does not allow you to specify a couple of key BLAST parameters: -v (number of hit descriptions to display) and -b (number of alignments to display). Setting each of these to 1 would show you only the first hit.
Batch BLAST generally requires that you set up BLAST locally. You would have to download unaligned sequences in fasta format from this location. BLAST databases are generated using the program formatdb, part of the BLAST executables package available from NCBI. It's not too difficult; there are plenty of questions and answers regarding local BLAST configuration at this site.
An alternative might be to use an aligner such as BLAT: see executables and source at Jim Kent's site. This will allow you to align your queries with the Greengenes sequences (both in fasta format), in memory. You'll need to look at the headers in the Greengenes sequence file to make sure they contain the information you need in the output.