Answers.Body: <p>You can opt for a similarity matrix as output (<a href="https://biology.stackexchange.com/questions/46049/how-to-interpret-percent-identity-matrix-created-by-clustal-omega">here is an example</a>). The fact that you would like to judge conservation &quot;relative to a given sequence&quot;, you can use this matrix to rank similarities of different sequences with respect to any of these sequences.</p>
  <p>I would advise visualizing these similarities, for example in terms of a heatmap, and seeing if anything stands out (with respect to your sequence of interest). And I would advise against selecting an arbitrary threshold (i.e. 90% or 95%), this would trigger questions based on the selection criteria of such a cutoff and this is understandable, such arbitrary cut-offs often do not mean much in biology.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-11-14T19:48:00.750Z
Answers.LastActivityDate: 2021-11-14T19:48:00.750Z
Answers.UserDisplayName: haci
Body: <p>I have 7 <code>RefSeq</code> accessions which I performed <code>multiple sequence aligment</code> on it using <code>CLUSTALO</code>. These are the following:</p>
  <pre><code>NC_026431.1
  NC_007363.1
  NC_004907.1
  NC_007377.1
  NC_007367.1
  NC_002016.1
  NC_026427.1
  </code></pre>
  <p>I input the fasta sequence of those 7 accessions on <code>CLUSTALO</code> under this <a href="https://www.ebi.ac.uk/Tools/msa/clustalo/" rel="nofollow noreferrer">link</a>. I get the result in either the <code>msf</code> format or <code>clustal</code> format with characters. The result looks like the following:</p>
  <pre><code>CLUSTAL O(1.2.4) multiple sequence alignment
  
  
  NC_002016.1      -------AGCGAAAGCAGGTAGATATTGAAAGATGAGTCTTCTAACCGAGGTCGAAACGT   53
  NC_007377.1      -------AGCAAAAGCAGGTAGATATTGAAAGATGAGCCTTCTAACCGAGGTCGAAACGT   53
  NC_007367.1      -------AGCAAAAGCAGGTAGATATTGAAAGATGAGCCTTCTAACCGAGGTCGAAACGT   53
  NC_004907.1      GGGGAATTCCAAAAGCAGGTAGATATTGAAAGATGAGTCTTCTAACCGAGGTCGAAACGT   60
  NC_026427.1      --------------------------------ATGAGTCTTCTAACCGAGGTCGAAACGT   28
  NC_007363.1      -------AGCAAAAGCAGGTAGATATTGAAAAATGAGTCTTCTAACCGAGGTCGAAACGT   53
  NC_026431.1      --------------------------------ATGAGTCTTCTAACCGAGGTCGAAACGT   28
                                                   ***** **********************
  </code></pre>
  <p>I'm aware that the <code>*</code> symbols means a highly conserved region and that's exatcly what I'm looking for , however I need the highly conserved regions relative to a specific accession, namely <code>NC_007367.1</code>. I'm not sure how to do that. I'm also not sure what the <code>-</code> represents.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-11-11T14:37:36.850Z
Comments.Text: https://www.ddbj.nig.ac.jp/faq/en/explain-three-symbols-e.html, https://abacus.bates.edu/bioinformatics1/clustalw2.html. **"highly conserved" is probably not an accurate way to judge "*".** All it means is that the position aligns perfectly across the input sequences, there is no statement about conservation or other evolutionary phenomena. clustal is only an alignment program.
Comments.UserDisplayName: Maximilian Press
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-11-11T16:14:03.827Z
Comments.Text: thanks, what would be the tool to find the conservative region then ? since CLUSTAL just gives a similarity estimation.
Comments.UserDisplayName: moth
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-11-11T17:26:09.113Z
Comments.Text: THere are various tools- depends a bit what your goal is in finding these positions. Simple visualizations that emphasize relative stability in alignments, e.g. here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3226196/. Gblocks is a somewhat more disciplined statistical approach, I am still unsure if it is exactly what you want: https://academic.oup.com/mbe/article/17/4/540/1127654, webserver here: http://molevol.cmima.csic.es/castresana/Gblocks_server.html
Comments.UserDisplayName: Maximilian Press
Tags: <multiple-sequence-alignment>
Title: find conservative regions relative to a specific accession
ThreadText: # find conservative regions relative to a specific accession
  
  (Asked by: username_0 on 2021-11-11)
  
  I have 7 `RefSeq` accessions which I performed `multiple sequence aligment` on it using `CLUSTALO`. These are the following:
  
  ```
  NC_026431.1
  NC_007363.1
  NC_004907.1
  NC_007377.1
  NC_007367.1
  NC_002016.1
  NC_026427.1
  
  ```
  
  I input the fasta sequence of those 7 accessions on `CLUSTALO` under this [link](https://www.ebi.ac.uk/Tools/msa/clustalo/). I get the result in either the `msf` format or `clustal` format with characters. The result looks like the following:
  
  ```
  CLUSTAL O(1.2.4) multiple sequence alignment
  
  NC_002016.1      -------AGCGAAAGCAGGTAGATATTGAAAGATGAGTCTTCTAACCGAGGTCGAAACGT   53
  NC_007377.1      -------AGCAAAAGCAGGTAGATATTGAAAGATGAGCCTTCTAACCGAGGTCGAAACGT   53
  NC_007367.1      -------AGCAAAAGCAGGTAGATATTGAAAGATGAGCCTTCTAACCGAGGTCGAAACGT   53
  NC_004907.1      GGGGAATTCCAAAAGCAGGTAGATATTGAAAGATGAGTCTTCTAACCGAGGTCGAAACGT   60
  NC_026427.1      --------------------------------ATGAGTCTTCTAACCGAGGTCGAAACGT   28
  NC_007363.1      -------AGCAAAAGCAGGTAGATATTGAAAAATGAGTCTTCTAACCGAGGTCGAAACGT   53
  NC_026431.1      --------------------------------ATGAGTCTTCTAACCGAGGTCGAAACGT   28
                                                   ***** **********************
  
  ```
  
  I'm aware that the `*` symbols means a highly conserved region and that's exatcly what I'm looking for , however I need the highly conserved regions relative to a specific accession, namely `NC_007367.1`. I'm not sure how to do that. I'm also not sure what the `-` represents.
  
  **Tags:** multiple-sequence-alignment
  
  > **Comments:**
  > **username_1**: https://www.ddbj.nig.ac.jp/faq/en/explain-three-symbols-e.html, https://abacus.bates.edu/bioinformatics1/clustalw2.html. **"highly conserved" is probably not an accurate way to judge "*".** All it means is that the position aligns perfectly across the input sequences, there is no statement about conservation or other evolutionary phenomena. clustal is only an alignment program.  
  > **username_0**: thanks, what would be the tool to find the conservative region then ? since CLUSTAL just gives a similarity estimation.  
  > **username_1**: THere are various tools- depends a bit what your goal is in finding these positions. Simple visualizations that emphasize relative stability in alignments, e.g. here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3226196/. Gblocks is a somewhat more disciplined statistical approach, I am still unsure if it is exactly what you want: https://academic.oup.com/mbe/article/17/4/540/1127654, webserver here: http://molevol.cmima.csic.es/castresana/Gblocks_server.html  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2021-11-14. Score: 2
  
  You can opt for a similarity matrix as output ([here is an example](https://biology.stackexchange.com/questions/46049/how-to-interpret-percent-identity-matrix-created-by-clustal-omega)). The fact that you would like to judge conservation "relative to a given sequence", you can use this matrix to rank similarities of different sequences with respect to any of these sequences.
  
  I would advise visualizing these similarities, for example in terms of a heatmap, and seeing if anything stands out (with respect to your sequence of interest). And I would advise against selecting an arbitrary threshold (i.e. 90% or 95%), this would trigger questions based on the selection criteria of such a cutoff and this is understandable, such arbitrary cut-offs often do not mean much in biology.
  
  
  ---
  
  