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Pileup/Consensus

Christophe Grundschober grund at cmu.unige.ch
Thu Jun 27 03:20:18 EST 1996


In article <4qsbgq$n72 at mark.ucdavis.edu>, caetano at FAUNA.UCDAVIS.EDU wrote:

> Hi there!
> 
> I want to compare differnet sequences for the same gene.  I know how to align
> multiple sequences with "Pileup".  The next thing I would like to do is to
> somehow visualize the differences between the sequences I am comparing, in
> other words, put dots where there's consensus and keep the actual bases where
> there's not.  Does anybody know how to do this?  I tried using "pretty",
on the
> "pileup" output file, but didn't get it to work (says the pileup file is not a
> GCG file..).
> 

You have to use pretty to do that. Type the following line (if GCG is
running on a UNIX system):

pretty -cons -dif -thr=1.5 -plu=2

when asked what sequence file you want to use, enter the name of your
pileup file:
pileup.msf{*}
dont forget the curly brackets.

Pretty will display the consensus of your sequences (-cons),  only the
differences from
the consensus will be shown (-dif). The threshold and plurality settings
of 1.5 and 2 are to make 
sure that every difference will be shown.

It took me a long time to figure this out the first time I used GCG.

Good luck

-- 
C. Grundschober
Transplantation Immunology Unit
Centre Medical Universitaire
1211 Geneve 4
Switzerland

grund at cmu.unige.ch



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