find conservative regions relative to a specific accession

Question

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.

Answer 1

You can opt for a similarity matrix as output (here is an example). 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.