text: user14140: I'm trying to compare proteins generated with prokka (from a genome) with blastp using a virulence factor database VFDB, and I want to use some parameters obtained from this paper:
  blastp option, top hit, ≥50% identity, ≥50% alignment length, E-value of < 10 - 5
  How can I specify those parameters on the command line?
  # create DB
  makeblastdb -in VFDB.fas -dbtype prot
  
  # run blast
  blastp -query my.faa -db VFDB.fas -out results.txt .....
  
  any suggestion?
  
  user4282: You can use these options:
  blastp -query my.faa -db VFDB.fas \
         -perc_identity 50 -outfmt 6 \
         -evalue 10e-5 -out results.txt
  
  Then select the 5th column, qlen, and the 13th columns, slen, and get the percentage higher than 50.
  awk  -F'\t' '{ if ($NF >= 50) printf "%s\t%.2f\n", $0 , ($2/$5)*100 }' result.txt
  
  Check the documentation for the full -outfmt column names with blast -help
  
original_text: 14140: <p>I'm trying to compare proteins generated with prokka (from a genome) with blastp using a virulence factor database <a href="http://www.mgc.ac.cn/VFs/download.htm" rel="nofollow noreferrer">VFDB</a>, and I want to use some parameters obtained from this <a href="https://journals.asm.org/doi/epdf/10.1128/mBio.02852-18" rel="nofollow noreferrer">paper</a>:</p>
  <p><code>blastp option, top hit, ≥50% identity, ≥50% alignment length, E-value of &lt; 10 - 5</code></p>
  <p>How can I specify those parameters on the command line?</p>
  <pre><code># create DB
  makeblastdb -in VFDB.fas -dbtype prot
  
  # run blast
  blastp -query my.faa -db VFDB.fas -out results.txt .....
  </code></pre>
  <p>any suggestion?</p>
   4282: <p>You can use these options:</p>
  <pre><code>blastp -query my.faa -db VFDB.fas \
         -perc_identity 50 -outfmt 6 \
         -evalue 10e-5 -out results.txt
  </code></pre>
  <p>Then select the 5th column, <em>qlen</em>, and the 13th columns, <em>slen</em>, and get the percentage higher than 50.</p>
  <pre><code>awk  -F'\t' '{ if (<span class="math-container">$NF &gt;= 50) printf "%s\t%.2f\n", $</span>0 , (<span class="math-container">$2/$</span>5)*100 }' result.txt
  </code></pre>
  <p>Check the documentation for the full <code>-outfmt</code> column names with <code>blast -help</code></p>
  