Hi,
Does anybody know what website can do multiple protein sequence alignment of highly similar sequences that would hide identical amino acids and show them only as e.g. dots - basically this more clearly shows differences - I have seen it in few papers but have no clue how they did it and there is no reference.
Ideally top sequence full and numbered and sequences underneath will show only differences from the top sequence.
Some programs I tried can colour identities dark for example but that's still bit messy.
Thank you all! Have been searching for this everywhere... :-/
Best,
Ondrej
Most multiple sequence alignment viewers have this feature built in. You can do the alignment with any program you like, or you can use the programs that are usually built in to the alignment viewer. Then after the protein sequences are aligned you select to "view identity to top sequence as a dot". For Mac, I recommend AliView, but MEGA and many other phylogenetics packages also include an alignment viewer. For Windows, I recommend BioEdit, but there are also many other choices.
http://ormbunkar.se/aliview/
http://www.mbio.ncsu.edu/BioEdit/bioedit.html
The software is free, very easy to install, and you can adjust the alignment, if you spot places wehre the program did it wrong. AliView has MUSCLEand MAFFT alignment built in. BioEdit has CLUSTAL and some other alignment tools built in, I think. I usually do alignment first, outside the viewer.
Thank you so much Brian!
Have been looking for this for hours - was hoping that some of the web services would do - it seems like COBALT - NCBI is supposed to be able to show identities as dots but it was buggy for me - I checked it and nothing happened (in Firefox).
I installed BioEdit and it worked well! I had an old ClustalX but that didn't seem to do that.
Thanks again and have a great weekend!
Best,
Ondrej
Use bioedit software. It is easy and can give you the image like:
https://media.springernature.com/full/springer-static/image/art%3A10.1186%2F1471-2164-15-1014/MediaObjects/12864_2014_Article_6830_Fig7_HTML.jpg
HI,
I use this: https://www.ebi.ac.uk/Tools/msa/clustalo/ For protein:
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