Answers.Body: <p>Smith-Waterman is guaranteed to give you the best alignment given your choice of substitution matrix.  For a few such tiny sequences, it's what I would use.  Many implementations exist.</p>
  
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Answers.UserDisplayName: Edward Kirton
Answers.Body: <p>blastn should be able to output this format of alignment result, using the <code>--outfmt 0</code> option</p>
  
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Answers.Body: <p>Is there any particular reason why you don't want a BAM output format? If the sequences are sufficiently long, then the CIGAR field from the SAM output of minimap2 could be used:</p>
  
  <pre><code>minimap2 -a seq1.fa seq2.fa | samtools view | awk '{print $6}'
  </code></pre>
  
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Answers.Body: <p>Perhaps you could use something like <code>SearchIO</code> to parse the output of BLAST, to get the desired alignment attributes: <a href="https://biopython.org/DIST/docs/api/Bio.SearchIO.BlastIO-module.html" rel="nofollow noreferrer">https://biopython.org/DIST/docs/api/Bio.SearchIO.BlastIO-module.html</a></p>
  
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Answers.UserDisplayName: Alex Reynolds
Body: <p>I have two sequences, say AAAGCTCGAGG and AAAGCGAGG. I need a convenient tool which shows me insertions or deletions between these, i.e. in this case something like</p>
  
  <pre><code>AAAGCTCGAGG
  |||||  ||||
  AAAGC  GAGG
  2bp deletion starting at base pair 5
  </code></pre>
  
  <p>and also insertions such as</p>
  
  <pre><code>AAAGCTC GAGG
  ||||||| ||||
  AAAGCTCTGAGG
  1bp insertion at base pair 7
  </code></pre>
  
  <p>Does something like that exist? Blastn finds the alignment of course, but only outputs the <em>number</em> of gaps, not their <em>position</em>. I guess I could parse a pileup, but do not want to create a bam file from one of the sequences first, so samtools seems to be out. Any further ideas?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-10-18T06:56:48.640Z
Comments.Text: IMO you need to write custom code. I just done this (again) via pandas, albeit elegant its a lot of code. Its quite easy to do via Perl5.
Comments.UserDisplayName: M__
Tags: <samtools><indel><blastn>
Title: Find indels between two short sequences
ThreadText: # Find indels between two short sequences
  
  (Asked by: username_0 on 2019-09-16)
  
  I have two sequences, say AAAGCTCGAGG and AAAGCGAGG. I need a convenient tool which shows me insertions or deletions between these, i.e. in this case something like
  
  ```
  AAAGCTCGAGG
  |||||  ||||
  AAAGC  GAGG
  2bp deletion starting at base pair 5
  
  ```
  
  and also insertions such as
  
  ```
  AAAGCTC GAGG
  ||||||| ||||
  AAAGCTCTGAGG
  1bp insertion at base pair 7
  
  ```
  
  Does something like that exist? Blastn finds the alignment of course, but only outputs the *number* of gaps, not their *position*. I guess I could parse a pileup, but do not want to create a bam file from one of the sequences first, so samtools seems to be out. Any further ideas?
  
  **Tags:** samtools, indel, blastn
  
  > **Comments:**
  > **username_1**: IMO you need to write custom code. I just done this (again) via pandas, albeit elegant its a lot of code. Its quite easy to do via Perl5.  
  
  ---
  
  ## 4 answers
  
  ### Answer by username_2 on 2019-10-23. Score: 1
  
  Smith-Waterman is guaranteed to give you the best alignment given your choice of substitution matrix. For a few such tiny sequences, it's what I would use. Many implementations exist.
  
  
  ---
  
  ### Answer by username_3 on 2019-09-16. Score: 0
  
  blastn should be able to output this format of alignment result, using the `--outfmt 0` option
  
  
  ---
  
  ### Answer by username_4 on 2019-11-22. Score: 0
  
  Is there any particular reason why you don't want a BAM output format? If the sequences are sufficiently long, then the CIGAR field from the SAM output of minimap2 could be used:
  
  ```
  minimap2 -a seq1.fa seq2.fa | samtools view | awk '{print $6}'
  
  ```
  
  
  ---
  
  ### Answer by username_5 on 2019-09-16. Score: 0
  
  Perhaps you could use something like `SearchIO` to parse the output of BLAST, to get the desired alignment attributes: <https://biopython.org/DIST/docs/api/Bio.SearchIO.BlastIO-module.html>
  
  
  ---
  
  