<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>

CC BY-SA 4.0
2021-11-14T19:48:00.750Z
2021-11-14T19:48:00.750Z
haci
<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>

CC BY-SA 4.0
2021-11-11T14:37:36.850Z
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.
Maximilian Press
CC BY-SA 4.0
2021-11-11T16:14:03.827Z
thanks, what would be the tool to find the conservative region then ? since CLUSTAL just gives a similarity estimation.
moth
CC BY-SA 4.0
2021-11-11T17:26:09.113Z
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
Maximilian Press
<multiple-sequence-alignment>
find conservative regions relative to a specific accession
# 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. 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  

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## 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.


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