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Separating out the consensus from lineup

Rodrigo Lopez rodrigol at biomaster.uio.no
Wed Feb 16 04:00:59 EST 1994


In article <2jrgdf$pb0 at gaia.ucs.orst.edu>, masrelia at ava.bcc.orst.edu (Malin Masreliez) writes:
|> Hello -
|> 
|> I was wondering if there is an easy way to save the consensus
|> sequence generated by lineup in a separate file (in GCG format)
|> so it can be used as input to other programs.  Editing the
|> alignment file is a drag...
|> 
|> Malin
|> ---------------------------------------------------------------
|> Malin Masreliez				masrelia at bcc.orst.edu	
|> Center for Gene Research		
|> Oregon State University
|> ---------------------------------------------------------------
|> 

You can try this approach:

Load the lineup file into Pretty with the following qualifiers:

% pretty @pileup.msf{*} -consensus -ugly
This will generate a consensus sequence and write each sequence
into a file with the extension '.ulgy'. Your consensus sequence is
likely to be called 'pileup.ulgy' if you generated the consensus
using LineUp. Note that the consensus sequence will contain gaps
and that certain GCG programs don't like these in their input
sequences.

R:)

-- 
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* RODRIGO LOPEZ SERRANO  rodrigol at biomed.uio.no - rodrigol at biotek.uio.no  * 
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