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Color code protein sequence alignment result to a reference sequence in black and white

Is there a software that would allow me to color coding my protein sequence alignment result to a reference sequence (see below image)?

The first row is my reference sequence, and I want to highlight amino acid residues in the other rows that are identical to my reference sequence.

sequence alignment

alignment
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updated by Suzanne Suzanne • written by tsaiy5 • tsaiy5

5 answers

Try Jalview

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written by shenwei356 shenwei356

ADOMA if you use linux.

https://sourceforge.net/projects/adoma/

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written by Benn Benn

I use Windows and have tried several softwares, including Jalview. Most softwares, like Jalview, allow me to color code according to amino acid properties or conservation. However, I can't figure out how to color the sequences according to the reference sequence (first row).enter image description here

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written by tsaiy5 • tsaiy5

In "JalView" --> Right click on the name of the sequence you want to set as reference. In the second option (name of the sequence selected) in the menu that opens choose "set as reference". After that choosing "above identity threshold" in the menu above may get you closer to what you want.

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written by GenoMax GenoMax

I just figure this out in SeaView4.

Basically, the software allows me to select a reference sequence and omit residues of the same amino acid in the alignment. This is not exactly what I was looking for at the beginning, but it serve the same purpose. So, for me, the problem is solved. But thanks shenwei356 & b.nota for suggestions!

enter image description here

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written by tsaiy5 • tsaiy5

Yep Seaview was going to be my suggestion.

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written by Joe Joe

There is Jalview video demonstrating icolouring sequences at https://youtu.be/b0M0eQf6qFY, Jalview can be accessed from http://www.jalview.org/

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written by Suzanne Suzanne

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