text: user4145: 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?
  
  user2436: 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.
  
original_text: 4145: <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>
   2436: <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>
  