Body: <p>I'm using BLAT to align DNA sequences between similar species, and having trouble setting the parameters to return only significant matches along the 50bp query lengths.</p>
  
  <p>Using <code>-tilesize=11 -minMatch=3 -minScore=30 -maxGap=2</code> my understanding is that it should return alignments with at least 3 non-overlapping tiles of 11 bases, so 33 bases minimum, with gaps of up to 2 bases between tiles, and bitscore at least 30. Instead the output is showing alignments as short as 4 bases and bitscore as low as 8. </p>
  
  <p>I tried setting <code>-minMatch=5</code> which should not find any 55bp matches in my 50bp queries, but even that gives a handful of results, with alignment length as low as 6. </p>
  
  <p>Can anyone enlighten me on the disconnect here? Thank you!</p>
  
  <p>EDIT: I think I see the problem: BLAT reports on a separate line for each fragment of the match. For example, one probe has a match from 1-41 and a match from 44-50, giving scores of 77 and 13. Now I will have a different set of questions!</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-05-24T12:54:02.063Z
Comments.Text: You're getting hits of only 5bp with BLAT, not BLAST? That should be much smaller than the word size used, how is that even possible? What BLAT implementation is this? Where can we find the explanation of what these options do exactly?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-05-25T17:37:48.877Z
Comments.Text: I'm running version 36. BLAT details are here: https://genome.ucsc.edu/goldenpath/help/blatSpec.html#blatUsage
Comments.UserDisplayName: Joanne
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-05-25T18:01:54.997Z
Comments.Text: Then I don't get it either. It shouldn't even be possible to get hits that short, just as you say. Could you [edit] your question and include an example query sequence so we can try and reproduce it?
Comments.UserDisplayName: terdon
Tags: <phylogenetics><blat>
Title: setting BLAT alignment parameters to give long matches
ThreadText: # setting BLAT alignment parameters to give long matches
  
  (Asked by: username_0 on 2020-05-22)
  
  I'm using BLAT to align DNA sequences between similar species, and having trouble setting the parameters to return only significant matches along the 50bp query lengths.
  
  Using `-tilesize=11 -minMatch=3 -minScore=30 -maxGap=2` my understanding is that it should return alignments with at least 3 non-overlapping tiles of 11 bases, so 33 bases minimum, with gaps of up to 2 bases between tiles, and bitscore at least 30. Instead the output is showing alignments as short as 4 bases and bitscore as low as 8.
  
  I tried setting `-minMatch=5` which should not find any 55bp matches in my 50bp queries, but even that gives a handful of results, with alignment length as low as 6.
  
  Can anyone enlighten me on the disconnect here? Thank you!
  
  EDIT: I think I see the problem: BLAT reports on a separate line for each fragment of the match. For example, one probe has a match from 1-41 and a match from 44-50, giving scores of 77 and 13. Now I will have a different set of questions!
  
  **Tags:** phylogenetics, blat
  
  > **Comments:**
  > **username_1**: You're getting hits of only 5bp with BLAT, not BLAST? That should be much smaller than the word size used, how is that even possible? What BLAT implementation is this? Where can we find the explanation of what these options do exactly?  
  > **username_0**: I'm running version 36. BLAT details are here: https://genome.ucsc.edu/goldenpath/help/blatSpec.html#blatUsage  
  > **username_1**: Then I don't get it either. It shouldn't even be possible to get hits that short, just as you say. Could you [edit] your question and include an example query sequence so we can try and reproduce it?  
  
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  ## 0 answers
  
  