Question: How To Obtain The Consensus Sequence From A Clustalo Result.
3
gravatar for muthurikim
6.1 years ago by
muthurikim30
muthurikim30 wrote:

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!!

msa clustalw alignment clustalo • 10k views
ADD COMMENTlink modified 4.7 years ago by Michael Dondrup46k • written 6.1 years ago by muthurikim30
4
gravatar for Joseph Hughes
6.1 years ago by
Joseph Hughes2.7k
Scotland, UK
Joseph Hughes2.7k wrote:

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. the screenshot You can then paste your consensus sequence into a text editor or your primer design program.

ADD COMMENTlink written 6.1 years ago by Joseph Hughes2.7k
3
gravatar for Hamish
6.1 years ago by
Hamish3.1k
UK
Hamish3.1k wrote:

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:

ADD COMMENTlink written 6.1 years ago by Hamish3.1k
2

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

ADD REPLYlink modified 5.5 years ago • written 5.5 years ago by andre20
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1350 users visited in the last hour