Welcome, Guest. Please Login or Register
UGENE Bulletin Board
  Welcome to our forum.
  HomeHelpSearchLoginRegister  
 
 
Page Index Toggle Pages: 1
How to get translation of consensus after CAP3 assembly? (Read 11134 times)
May 11th, 2013 at 4:06am

vixen sjlin   Offline
YaBB Newbies

Posts: 8
*
 
Hi there:

I am beginning to use Ugene and so far I love it, thanks a lot for creating such great tool!

One question:  I tried to assemble long reads by "Contig assembly by CAP3" and like it.  However, is it possible to get the 6 ways translation of the consensus sequence listed below the DNA assembled contig?  That's very useful for cDNA cloning.

PS. I tried right-click --> export -->amino translation of alignment rows, but what I get is not what I want.  I prefer the amino acids codes listed under the assembled DNA contig sequence so that we can exam the reading frames.

Thanks a lot and have a nice weekend!
 
IP Logged
 
Reply #1 - May 12th, 2013 at 9:39pm

Konstantin Okonechnikov   Offline
Global Moderator

Posts: 173
*****
 
There is currently no visualization available for 6 frames translations of the consensus sequence in Multiple Alignment Editor.

What one can do: copy consensus sequence (context menu Copy->Copy consensus sequence), than create a new sequence (File -> New document from text).

There is one detail: the consensus will contain symbols such as '+' when there is equal probability for the same base to be one or another nucleotide.  In order to get rid of these '+'-symbols and keep the reading frame, one has to replace unknown symbols with 'N', when using option to create new document from text.
 
IP Logged
 
Reply #2 - May 23rd, 2013 at 1:08am

vixen sjlin   Offline
YaBB Newbies

Posts: 8
*
 
It is definitely doable to copy consensus and translate elsewhere, but doing that will easily loss visual alignment between the sequencing contigs and amino acids, which is important for molecular cloning of protein expression.  It would be nice if Ugene can consider to add this function, even translate some useless + in consensus into something like * in amino acids.
 
IP Logged
 
Page Index Toggle Pages: 1