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2 hours ago by

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 NCBIWWW function of the Bio.Blast module of Biopython
  • accessing the BLAST+ program via theNcbiblastpCommandline function of the Bio.Blast.Applications module of Biopython and using the - remote argument

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?

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