How to talk homology with pileup

Petr Jordan jordan
Thu Nov 30 10:07:49 EST 1995

| Petr Jordan, System Manager                                             |
|              Max Planck Institute for Biochemistry, MIPS                |
|              Am Klopferspitz 18A , D-82512 Martinsried, Germany         |
| E-mail: jordan at mips.embnet.org                                          |
| Phone: ++(89)-8578-2664		Fax.: ++(89)-8578-2655            |
|                                                                         |
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From: duhaimj at IRCM.UMontreal.CA ("SI-Johanne Duhaime")
Newsgroups: bionet.software.gcg
Subject: How to talk homology with pileup
Date: 7 Nov 1995 13:07:45 -0800
Organization: BIOSCI International Newsgroups for Molecular Biology
Message-ID: <951107160416.ZM7663 at si05.IRCM.UMontreal.CA>

Good afternoon,

I have a question that is often asked by researchers of our site.

Let's say that you do a pileup with a set of sequences.  How to talk 
homology with the result? Let me make that clearer. With the program gap 
you can say: in that segment of the two sequences you have xx% of 
similarity. But with pileup you do not have such a result.  You can use 
Plotsimilary to have an idea of the similarity but it is a graphical 
Do you have any suggestion on that. When you publish how do you point 
out the similarity?
Thank you very much for your help.

Johanne Duhaime
Duhaimj at ircm.umontreal.ca

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