I have a list of 189 Accession numbers for 16s rRNA, how can I batch BLAST these to find which species they are closest too? I tried this server: http://greengene.uml.edu/programs/NCBI_Blast.html but the output that it gives me is huge for each accession number. I'm more looking for the a program that will give me a summary so I can quickly see the species that most match these 189 sequences.
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.
It's a web-service that allows you to BLAST sequences, filter results accordingly, then export annotations etc. (Been a long time since I've used it, so not sure if it'll work for your case)
EDIT: Went back and found my PLAN account details - it'll definitely do what you want but you have to upload FASTA files (not just IDs). Once you fetched the FASTA sequences and clicked "Do BLAST" it's pretty straightforward.