Answers.Body: <p>@Matteo Ferla wrote in the comments,</p>
  <blockquote>
  <p>It sounds like you'd want a MSA of the whole set and not a set of pairwise ones. If global MSA is what you actually want, try ebi.ac.uk/Tools/msa/muscle. Then to trim the ends before phylogeny there are dozens of tools.</p>
  </blockquote>
  <blockquote>
  <p>The reason is because Blast aligns locally, i.e. a window, while a global alignment is the whole entirety of the sequence</p>
  </blockquote>
  
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Answers.Body: <p>BLAST isn't appropriate for multiple sequence alignment.
  BLAST generates pairwise alignments. Furthermore, the aligning regions shown in a BLAST report only include subsets of the hit sequences.</p>
  <p>To create multiple sequence alignment of hits you want to:</p>
  <ul>
  <li>run blast</li>
  <li>extract the hit sequences</li>
  <li>perform multiple-sequence-alignment (e.g., using MAFFT)</li>
  </ul>
  <p>Extracting hit sequences can be done using the command-line. Check the docs for <code>blastdbcmd</code>.</p>
  <p>If you prefer a point-and-click interface, you can also do this using my lab's <a href="https://sequenceserver.com" rel="nofollow noreferrer">SequenceServer BLAST software</a> by simply selecting the hits that you want to retain, and in the <strong>Download</strong> section, clicking &quot;FASTA of selected hits&quot;. Or if you want all of them, click &quot;FASTA of all hits&quot;.</p>
  <p><a href="https://sequenceserver.com/" rel="nofollow noreferrer"><img src="https://sequenceserver.com/img/blast-setup/normal-blast-result.png" alt="Download hits from BLAST report " /></a></p>
  
Answers.ContentLicense: CC BY-SA 4.0
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Answers.Text: Please add a statement stating that your lab created this software that you're posting about on multiple threads.
Answers.UserDisplayName: Ram RS
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Body: <p>To generate aligned protein sequence truncate to the same length, I use blastp in biopython for MSA. I have multiple queries and one subject sequence. However, the alignment never returns the same length.</p>
  <p>How can I align all sequences altogether, thus resulting in a set of sequences of the same length?</p>
  
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Comments.UserDisplayName: M__
Tags: <python><blastp>
Title: Blastp MSA to the same length
ThreadText: # Blastp MSA to the same length
  
  (Asked by: username_0 on 2020-08-09)
  
  To generate aligned protein sequence truncate to the same length, I use blastp in biopython for MSA. I have multiple queries and one subject sequence. However, the alignment never returns the same length.
  
  How can I align all sequences altogether, thus resulting in a set of sequences of the same length?
  
  **Tags:** python, blastp
  
  > **Comments:**
  > **username_1**: Please consider accepting/upvoting the answers below.  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_1 on 2023-09-12. Score: -1 | Accepted answer
  
  @Matteo Ferla wrote in the comments,
  
  > It sounds like you'd want a MSA of the whole set and not a set of pairwise ones. If global MSA is what you actually want, try ebi.ac.uk/Tools/msa/muscle. Then to trim the ends before phylogeny there are dozens of tools.
  
  > The reason is because Blast aligns locally, i.e. a window, while a global alignment is the whole entirety of the sequence
  
  
  ---
  
  ### Answer by username_2 on 2021-12-19. Score: 2
  
  BLAST isn't appropriate for multiple sequence alignment.
  BLAST generates pairwise alignments. Furthermore, the aligning regions shown in a BLAST report only include subsets of the hit sequences.
  
  To create multiple sequence alignment of hits you want to:
  
  * run blast
  * extract the hit sequences
  * perform multiple-sequence-alignment (e.g., using MAFFT)
  
  Extracting hit sequences can be done using the command-line. Check the docs for `blastdbcmd`.
  
  If you prefer a point-and-click interface, you can also do this using my lab's [SequenceServer BLAST software](https://sequenceserver.com) by simply selecting the hits that you want to retain, and in the **Download** section, clicking "FASTA of selected hits". Or if you want all of them, click "FASTA of all hits".
  
  [![Download hits from BLAST report ](https://sequenceserver.com/img/blast-setup/normal-blast-result.png)](https://sequenceserver.com/)
  
  > **Comments:**
  > **username_3**: Please add a statement stating that your lab created this software that you're posting about on multiple threads.  
  
  ---
  
  