I have been working on aptamers, which are nucleotide sequences. They bind to various targets, in my case a particular cell surface receptor. The people associated with the project performed SELEX and they have selected sequences that have affinity for the target. My advisor believes that the sequences could share a particular binding pocket (consensus sequence).

The sequences are mostly 40 nucleotides long but some of them are shorter or longer in length. I have to aligned the sequences in an attempt to identify sequences containing a consensus site. So far I have used both Clustal Omega and Multalin, but the results from them are pretty inconsistent.

Clustal Omega Alignment:

Alignment using Clustal Ω

Alignment using Multalin

I also aligned a few sequences using a pairwise alignment method, but I found few similar regions among the sequences.

How do I interpret these results from Clustal Omega and Multalin?

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    $\begingroup$ Welcome to SE Biology. Please take the Tour (we can see you haven’t) and read about asking questions here. You have explained your problem well, but seem to want us to solve it for you. However we need to know what you make of it yourself. Do you know why alignments by different programs are different? You need to read about MSA and the particular algorithms behind the ones you have used. Which one do you think has aligned the sequences better? No reading there — use your eyes. And has the better alignment found a consensus site? Again, use your own judgment and that of your advisor. $\endgroup$
    – David
    Jul 12 '19 at 18:18
  • $\begingroup$ I made some edits that I hope clarify your question, but it seems to me that you might want to ask a different question — "What alignment method would work best for finding a consensus from these sequences?" $\endgroup$
    – tyersome
    Jul 12 '19 at 18:21
  • $\begingroup$ You might want to look at partial order alignment. $\endgroup$
    Jul 12 '19 at 23:07
  • $\begingroup$ @tyersome Should I delete the question and ask again? $\endgroup$ Jul 15 '19 at 5:54
  • $\begingroup$ I don't think that's necessary — you can just edit your post. However, I encourage you to follow up on @WYSIWYGs suggestion — they show signs of having significant expertise in bioinformatics! $\endgroup$
    – tyersome
    Jul 15 '19 at 16:16

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