I have snippets of protein sequences and I need to find out to which accession numbers of the nr database they belong.
So far I tried to automate this process in the following way:
- accessing the NCBI webserver directly via the
NCBIWWWfunction of the
Bio.Blastmodule of Biopython
- accessing the BLAST+ program via the
NcbiblastpCommandlinefunction of the
Bio.Blast.Applicationsmodule of Biopython and using the
But both ways basically take forever. Do any of you have an idea how I can automate this without having to download the nr database of NCBI? Or is this really the only way?