Question: Which multiple sequence alignment algorithm should be used for small dataset?
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gravatar for macbas
5 weeks ago by
macbas0
macbas0 wrote:

Dear all,

I have just six protein sequences from the one family, but they are pretty distantly related. As you know, there is a bunch of algorithms that may align them, but for sure all of them have pros and cons (for example one is more accurate but slower and other is designed for big sets of sequences with high-speed optimization). Do you have any recommendations which one fits my needs? Thanks in advance!

alignment • 115 views
ADD COMMENTlink modified 5 weeks ago by Shalu Jhanwar460 • written 5 weeks ago by macbas0
1

If you have just 6 proteins (and you know for sure that they are related even though distantly) you can easily try a few options out. Depending on length etc some may work better than others.

ADD REPLYlink written 5 weeks ago by genomax89k

Thank you very much. Actually I have already done this. The results differ a bit, and since I want to decide which AAs to mutate, I wonder if some of the algorithms might be considered as more "trustable" for my need. But it seems there is no simple answer for that. Anyway, thank you for your help!

ADD REPLYlink written 5 weeks ago by macbas0
1

In that case I suggest that you pay particular attention to residues that are known to be critical for function (binding, active site etc). If the alignments don't look right in that region then you may want to manually edit them (within reason) to see if there are changes to these residues you need to pay attention to. Adding additional sequences (related) may offer support for the relationships you are observing.

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by genomax89k

I will act accordingly. Once again, thanks!

ADD REPLYlink written 5 weeks ago by macbas0
2
gravatar for Shalu Jhanwar
5 weeks ago by
Shalu Jhanwar460
Switzerland
Shalu Jhanwar460 wrote:

Have a look at MUSCLE aligner for this purpose. Given there are only a few sequences, you can try the web version.

ADD COMMENTlink written 5 weeks ago by Shalu Jhanwar460
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