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Pileup/Consensus

Francois Jeanmougin pingouin at crystal.u-strasbg.fr
Thu Jun 27 02:43:33 EST 1996


In article <4qsbgq$n72 at mark.ucdavis.edu>,
	caetano at FAUNA.UCDAVIS.EDU writes:
>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..).
>
>Any help will be appreciated.
>
>Thanks
>
>
>Alex
>
	I think that you make a mistake in the command line. You have a pileup
file called somthing like toto.msf. you must use :
	pretty toto.msf{*}
	This is to tell the pretty programm that he will find an msf formated
file and should take all the sequences in it.

					hope this help
					If not, more support by e-mail.
					Francois.

-- 
Francois Jeanmougin
Service de bioinformatique / bioinformatic service
IGBMC 
BP 163 
67404 Illkirch France
tel : (33) 88 65 32 71
e-mail : jeanmougin at igbmc.u-strasbg.fr

Les petits pois sont rouges (STTELLLA)




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