How To Obtain The Consensus Sequence From A Clustalo Result.
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8.8 years ago
muthurikim ▴ 40

Hi good people,

I am trying to get the consensus sequence from the same genes so that i can use it to design primers. I have aligned them in ClustalO and can see the sequence in JalView. How do I export it to a primer designing program? I have tried copy and paste but it does not seem to work.

I have tried aligning them in CAP3 but I don't get any results.

Help!!

clustalw msa alignment clustalo • 14k views
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8.8 years ago
Joseph Hughes ★ 2.9k

From JalView you can copy the consensus sequence using right-click on the word consensus near the consensus histogram (on mac it is the command key (⌘) and click). This opens up a menu where you select the Copy Consensus Sequence as seen in the screenshot. You can then paste your consensus sequence into a text editor or your primer design program.

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8.8 years ago
Hamish ★ 3.2k

One option would be to use the EMBOSS tool cons to generate the consensus sequence from the alignment.

The EMBOSS tools are available on-line in a wide range of places, for example:

If you want to install EMBOSS locally you have a number of options:

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Note that in newer ubuntu version, emboss cons is renamed to em_cons. it took me a while to figure this one out. source