After doing alignment of some protein sequences using Clustal Omega, I got the result that I have been attached herewith. I am seeking exparts opinion so that can find a good explanation of the result.
On first sight, all sequences look equal. I'd change the colouring scheme to highlight differences from the consensus sequence, this would make interpretation easier.
Dear Shahina Akter ,
No personal experience with Clustal Omega but my impression is that it might be a ‘fancy’ and state-of-the-art alignment program but not that user-friendly.
Unless your sequences are (almost) identical I feel as said by Engelbert Buxbaum that your sequences are (remarkably) identical. My impression is that your alignment is the (end-)result of some serious re-alignment done by the program (or due to some unintended command you gave) which resulted in removal of all types of details about the ‘gaps’ and stretches of regions that are removed because for example one sequence is shorter than the other.
I suggest you to use a way more simple (and user-friendly) program like ClustalW first (and perhaps first align two sequences), see for an example:
Article Identification and in silico analysis of helical lipid bindi...
T-Coffee is one you could consider too. Once you have these results you might (if still relevant) go back to Clustal Omega.
Best regards.
Thank you, Dr. Engelbert Buxbaum and Rob Keller for your response. I am concerned about that SNP portion (or deletion).
This is a study of SARS-CoV-2, which have been sequenced in my laboratory. The sequence of spike protein was compared with that of Wuhan. According to this figure, we got a deletion in sample number 2020-6-7-1-167. Whereas in the secondary structure of that particular protein shows N wherein Wuhan it is S (Picture attached). That is not clear to me.
Dear Shahina Akter ,
If I understand your question correctly the answer is quite simple, the secondary structure result ‘simply’ omits the deleted position (it is there but you cannot see it in the result).
So, the secondary structure prediction analysed the region including the deletion …PGTNT-NQVAVL… but shows it as …PGTNTNQVAVL
Hi Shahina,
As Rob Keller has said, the order of your sequence is PGTNT-NQVAVLY
Actually, the deleted "S" is replaced by a dash, which this dash is ignored in your results.
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