need aligner help

Eric Cabot ecec at quads.uchicago.edu
Thu May 28 10:17:35 EST 1992

In article <9205280222.AA06284 at evolution.genetics.washington.edu> joe at GENETICS.WASHINGTON.EDU (Joe Felsenstein) writes:
>We have no standard for how gaps are to be represented in sequences (that
>I know of, anyway).  I like to use "-" for gap.  GCG uses periods, whereas
>other people have on occasion used them to mean "the same as in the first
>sequence", and so do I.  Some folks use blanks, other just skip over them as
>cosmetic spacing characters.
>Is it wise to encourage "-" to mean something other than "gap"?  Is there a
>standard out there that I don't know about, and if so what does it say?
I wish there WAS a standard character for gaps (and also "same as the first
sequence").  Until I started encountering GCG users I could get by with
"-" for gaps. Now all of my programs need to include a prompt for the
gap character, which means that the user must remember what character was

Things can get really confusing when comparing GCG and non-GCG
outputs of multiple alignments that have lots of gaps and use a "same
as above feature".  I'll look at one of those and say "Gee, look at all
the gaps" and one of my co-workers will say "no, the gaps are the periods".
It's enough to drive a programmer back to the lab bench -- for the ethanol!

    Eric Cabot                      CHICAGO: City of fire, wind and water. 
ecec at midway.uchicago.edu

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