How to talk homology with pileup

Jack Leunissen jackl at caos.kun.nl
Thu Dec 7 05:28:56 EST 1995

Petr Jordan <jordan> wrote:

>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?

I think I've posted this before, but in the EGCG package there is program
called HOMOLOGIES, which can calculate exactly what you want. Just run the
program with the -PERCENT option (/PERCENT on VMS) on your MSF, and it will
give you the percentage homology between sequences. By default, it uses 
IDENTITY scores to calculate the similarity between sequences, but this can
be changed to whatever you like.

The program calculates similarities or distances; the distance-output file
can be used directy with the PHYLIP package (J. Felsenstein, Seattle).


      Dr. Jack A.M. Leunissen. | CAOS/CAMM Center, Univ. of Nijmegen
      Email: jackl at caos.kun.nl | Toernooiveld
      Tel. : +31 24 365 22 48  | 6525 ED Nijmegen, The Netherlands
      Fax  : +31 24 365 29 77  | URL=http://www.caos.kun.nl/

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