I ran a local blastp on the nr database from NCBI and got 100,000 hits. I organized the ones I wanted to keep in excel and I have a text file of all of their headers/description lines. How do I use what I have to get all of the actual sequences from NCBI? This may be a batch entrez thing, or it may possibly be the exact opposite...either way I figured this is a very common issue people deal with but I couldn't find a concrete solution.
Perfect! Thank you very much. I was actually looking at this before but I wasn't entirely sure.
This might be a REALLY stupid question, but do I need to use the unformatted fasta nr database?
EDIT: I tested it out and learned that I can just use the formatted db I was using for blastp. Thanks again; your command example worked perfectly.