How to talk homology with pileup

Stephen Baird sbaird at mgcheo.med.uottawa.ca
Wed Dec 6 11:03:20 EST 1995

Petr Jordan (jordan) wrote:

: 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 
: output.
: 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

    I prefer to use the IDENTITY score of a gap alignment as the 
alignment in pileup are not optimized for each pair. For a visual 
representation of a bunch of sequences, pileup is good to use for 
publication. I also write a script to do a gap alignment of each 
combination of the sequences and parse out the alignment score into a 
file where I can put it in a matrix and refer to the scores in the 
text of a publication.  I think percent IDENTITY is easier for 
everyone to understand when referring to homology. Similarity requires 
one to know the parameters which make up the definition of "similarity".
The constraints used to make the alignment effect both the score for 
identity and similarity.

| Stephen Baird                        sbaird at mgcheo.med.uottawa.ca  | 
| Molecular Genetics                       tel: 613-738-3925         |
| Children's Hospital of Eastern Ontario   fax: 613-738-4833         |
| 401 Smyth Rd.                                                      |
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| K1H 8L1                                                            |

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