Body: <p>We are going to look at the likely N- and O- glycosylation sites within MUC16 (<a href="https://www.uniprot.org/uniprotkb/Q8WXI7/entry" rel="nofollow noreferrer">Q8WXI7 · MUC16_HUMAN</a>)§ by in house long-read DNA sequencing data (PacBio).</p>
  <p>Counting the number of tandem repeats is a task which could be done with bioinformatic tools like <code>ad-codeVNTR</code>as shown in the below figure. Another task is identifying mutations within these repeats. My question is: after predicting <code>glycosylation sites</code> using tools like <code>PA2DE</code> within these tandem repeats in <em>MUC16</em> gene, how could I identify any point mutations in these <code>glycosylation sites</code>?</p>
  <p>I googled a lot to get some idea; Shall we do germline analysis in <em>MUC16</em> glycosylation predicted sites? Is this what we should use to look at glycosylation sites that are ‘rejected’ to understand the sites that can’t be glycosylated (mutated)?</p>
  <p>Does anyone have such an experience how to identify mutation in glycosylation sites in MUC16 which known to have variable number tandem repeat (VNTR)?</p>
  <p><a href="https://i.sstatic.net/RBIzU.jpg" rel="nofollow noreferrer"><img src="https://i.sstatic.net/RBIzU.jpg" alt="enter image description here" /></a></p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-09-03T01:10:08.577Z
Comments.Text: If you write the exact rules, it's not difficult to write a regex function to find these. How many repeats? What does tandem mean? Is it without spaces, VNTRVNTRVNTR?
Comments.UserDisplayName: Supertech
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-09-03T10:57:31.063Z
Comments.Text: Thank you, counting the number of repeat is another task which could be done with bioinformatic tools like ad-codeVNTR. Another task is identifying mutations within these repeats. My question is after predicting glycosylation sites, how could I identify any point mutations in these glycosylation sites.
Comments.UserDisplayName: Zizogolu
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-09-03T11:58:55.657Z
Comments.Text: Please [edit] your question and clarify what you need and what you are working with:  What are your input data? Protein? DNA? Have you performed your own sequencing? Are you looking through published sequences? How do you define mutation, what is your reference? Doesn't code-adVNTR do exactly what you want? The image you show suggests it does, so isn't it already what you need?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-09-03T17:18:22.933Z
Comments.Text: Thank you I tried to edit my question. That would DNA long read sequencing done on human cancer cell lines
Comments.UserDisplayName: Zizogolu
Tags: <protein-structure><sequence-analysis><pacbio><mass-spectrometry>
Title: Finding mutations in glycosylation sites
ThreadText: # Finding mutations in glycosylation sites
  
  (Asked by: username_0 on 2023-09-03)
  
  We are going to look at the likely N- and O- glycosylation sites within MUC16 ([Q8WXI7 · MUC16\_HUMAN](https://www.uniprot.org/uniprotkb/Q8WXI7/entry))§ by in house long-read DNA sequencing data (PacBio).
  
  Counting the number of tandem repeats is a task which could be done with bioinformatic tools like `ad-codeVNTR`as shown in the below figure. Another task is identifying mutations within these repeats. My question is: after predicting `glycosylation sites` using tools like `PA2DE` within these tandem repeats in *MUC16* gene, how could I identify any point mutations in these `glycosylation sites`?
  
  I googled a lot to get some idea; Shall we do germline analysis in *MUC16* glycosylation predicted sites? Is this what we should use to look at glycosylation sites that are ‘rejected’ to understand the sites that can’t be glycosylated (mutated)?
  
  Does anyone have such an experience how to identify mutation in glycosylation sites in MUC16 which known to have variable number tandem repeat (VNTR)?
  
  [![enter image description here](https://i.sstatic.net/RBIzU.jpg)](https://i.sstatic.net/RBIzU.jpg)
  
  **Tags:** protein-structure, sequence-analysis, pacbio, mass-spectrometry
  
  > **Comments:**
  > **username_1**: If you write the exact rules, it's not difficult to write a regex function to find these. How many repeats? What does tandem mean? Is it without spaces, VNTRVNTRVNTR?  
  > **username_0**: Thank you, counting the number of repeat is another task which could be done with bioinformatic tools like ad-codeVNTR. Another task is identifying mutations within these repeats. My question is after predicting glycosylation sites, how could I identify any point mutations in these glycosylation sites.  
  > **username_2**: Please [edit] your question and clarify what you need and what you are working with:  What are your input data? Protein? DNA? Have you performed your own sequencing? Are you looking through published sequences? How do you define mutation, what is your reference? Doesn't code-adVNTR do exactly what you want? The image you show suggests it does, so isn't it already what you need?  
  > **username_0**: Thank you I tried to edit my question. That would DNA long read sequencing done on human cancer cell lines  
  
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  ## 0 answers
  
  