title: How to blastp with fasta file that contains ~50 sequences
body: <p>I'm trying to blastp multiple aminoacids sequences using biopython. I just can't seem to get it right and i cant figure out the handbook for how to do this. I have come up with the following:</p>
  <pre><code>open(&quot;proteins_PROT.fasta&quot;,&quot;r&quot;)
  
  from Bio.Blast.Applications import NcbiblastpCommandline
  cline = NcbiblastpCommandline(query=&quot;proteins_PROT.fasta&quot;, db=&quot;nr&quot;,
                            evalue=0.001, remote=True, ungapped=True)
  
  NcbiblastpCommandline(cmd='blastp', query=&quot;proteins_PROT.fasta&quot;, db='nr', evalue=0.001, 
  remote=True, ungapped=True)
  print(cline)
  blastp -query proteins_PROT.fasta -db nr -evalue 0.001 -remote -ungapped
  </code></pre>
  <p>How do i run a blastp result with multiple sequences in a fasta?</p>
  <p>Thank you</p>