How To Obtain The Consensus Sequence From A Clustalo Result.

Question

[muthurikim]

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!!

Answer 1

[Joseph Hughes]

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.

Answer 2

[Hamish]

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:

• http://emboss.bioinformatics.nl/
• http://bioinfo.nhri.org.tw/gui/
• http://imed.med.ucm.es/EMBOSS/
• http://wsembnet.vital-it.ch/soaplab2/

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

• On Debian based Linux distributions (e.g. Ubuntu, Linux Mint, Bio-Linux, etc.) the standard repositories include an EMBOSS package: emboss
• For RPM based Linux distributions (e.g. RedHat, Fedora, SuSE, etc.) packages are available: see http://rpm.pbone.net/index.php3?stat=3&search=EMBOSS
• Build from source. The source distribution is available from the EMBOSS web site, and can also be obtained from a mirror on the EMBL-EBI FTP site: ftp://ftp.ebi.ac.uk/pub/software/unix/EMBOSS

[andre]

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