Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-09-12T06:46:28.493Z
Answers.Text: Thanks so much for the help. one more questions. I use the outfmt 6, and it have the next columns: qseqid, sseqid, pident, length, mismatch, gapopen, qstart, qend, sstart, send, evalue, bitscore. in this case which columns do I have to use to determinate the percent of alignment length? , thanks so much
Answers.UserDisplayName: abraham
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-09-13T06:59:43.903Z
Answers.Text: you can configure outfmt 6 to produce a custom format, *qlen* and *slen* included, check the `blastp -help`
Answers.UserDisplayName: zorbax
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-09-10T07:59:33.120Z
Answers.LastActivityDate: 2021-09-11T12:24:37.607Z
Answers.LastEditDate: 2021-09-11T12:24:37.607Z
Answers.UserDisplayName: zorbax
Body: <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>
  
Tags: <blastp><makeblastdb>
Title: blastp option to compare with a personal database
ThreadText: # blastp option to compare with a personal database
  
  (Asked by: username_0 on 2021-09-10)
  
  I'm trying to compare proteins generated with prokka (from a genome) with blastp using a virulence factor database [VFDB](http://www.mgc.ac.cn/VFs/download.htm), and I want to use some parameters obtained from this [paper](https://journals.asm.org/doi/epdf/10.1128/mBio.02852-18):
  
  `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?
  
  **Tags:** blastp, makeblastdb
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2021-09-10. Score: 5 | Accepted answer
  
  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`
  
  > **Comments:**
  > **username_0**: Thanks so much for the help. one more questions. I use the outfmt 6, and it have the next columns: qseqid, sseqid, pident, length, mismatch, gapopen, qstart, qend, sstart, send, evalue, bitscore. in this case which columns do I have to use to determinate the percent of alignment length? , thanks so much  
  > **username_1**: you can configure outfmt 6 to produce a custom format, *qlen* and *slen* included, check the `blastp -help`  
  
  ---
  
  