Question: Consensus Sequence In Multiple Sequence Alignment- A Brief Idea And Representation
3
gravatar for Pals
6.1 years ago by
Pals1.3k
Finland
Pals1.3k wrote:

I am confused how the consensus sequence is generated. How can the parameters to calculate consensus sequence (if possible) be configured in programs like Jalview? Because, the default setting in Jalview (I used this program) does not seem to be useful to interpret consensus sequence. I would be interested for example, to ignore the positions that are under-represented in the alignment (having less than 10% coverage). In fact, I want to try the program that works best in working with consensus sequence.

I want to view the consensus sequence in such a format that consensus residue for position with lets say 70% conservation will show the amino acid and rest of the positions will be shown as X. Thus, the consensus sequence will be like. AGXXXXXXXEXXXT, where A,G and T are highly conserved residues in particular MSA position.

-Ksn

consensus multiple • 4.9k views
ADD COMMENTlink modified 3.3 years ago by madk00k320 • written 6.1 years ago by Pals1.3k
5
gravatar for Tancata
6.1 years ago by
Tancata200
Newcastle, UK
Tancata200 wrote:

The Seaview alignment editor/viewer does this - http://pbil.univ-lyon1.fr/software/seaview.html

Props -> Consensus and you can set the threshold, etc.

ADD COMMENTlink written 6.1 years ago by Tancata200

Thanks a lot. Similar is the program I was looking for.

ADD REPLYlink written 6.1 years ago by Pals1.3k

Do you have any idea on how threshold have an effect in generating consensus sequence?? I am quite convinced with the representation, however, using different threshold values, the length of consensus differs.

ADD REPLYlink written 6.1 years ago by Pals1.3k
0
gravatar for Larry_Parnell
6.1 years ago by
Larry_Parnell16k
Boston, MA USA
Larry_Parnell16k wrote:

A slight modification to consider is B for either asparagine (N) or aspartic acid (D) and Z for glutamine (Q) or glutamic acid (E).

ADD COMMENTlink written 6.1 years ago by Larry_Parnell16k
0
gravatar for madk00k
3.3 years ago by
madk00k320
Heidelberg
madk00k320 wrote:

Unipro UGENE includes a number of configurable consensus algorithms for multiple sequence alignments:

http://ugene.unipro.ru/documentation/manual/alignment_editor/overview/consensus.html 

Export of consensus is also available as command line tool.

 

ADD COMMENTlink written 3.3 years ago by madk00k320
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