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.