GCG: distances changing gap weights

Neal Dalton nrd at insitu.med.umn.edu
Mon Aug 29 11:31:19 EST 1994

David Mathog (mathog at seqvax.caltech.edu) wrote:
: In article <Cv5rJ5.Hqt at news.cis.umn.edu>, nrd at insitu.med.umn.edu (Neal Dalton) writes...
: >We would like to change the weight given to gaps vs nucleotides when
: >calculating distances using GCG's distance program.  Currently, gap

: Why, and to what?

We want gaps to have a 0.5 value.

: >mismatches are given the same weight as nucleotide mismatches.

: Well, yes for A vs. G, but no for T vs. Y, for instance.  Note that that
: weight is zero, so there need not be an explicit "." column in the table
: as GCG specifies that if the symbol isn't in the table, any comparison
: against it returns zero. 

I added a "." column to the table and it didn't change the values.

: >How can we do this?  I tried to add gaps to the dnadistances.cmp table,
: >but that didn't seem to work.

: It should have worked, take a look at the randomdna.cmp file for example.
: Possibly you need to run it through reformat to clean it up?

I did that and it just delete one line and didn't make a difference.

: On the off chance that there is some bug that precludes using a "." column/
: row you could edit the .MSF file that you're working on and convert all
: gaps to some other symbol, for instance, "Y".  Then edit a *copy* of the
: comparison table, changing all of the values in the Y associated columns/
: rows to be what you want for A vs. gap, G vs. gap, etc.  This assumes that
: you don't have any "Y" entries in your data. 

Interesting.  I could give it a try.


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