need aligner help

Joe Felsenstein joe at GENETICS.WASHINGTON.EDU
Wed May 27 21:22:01 EST 1992

Eric Mansell wanted to find an alignment program for Macs that showed:

>         For example... seq1 MAELAVIR
>                        seq2 --A---V-
>         instead of...  seq1 MAELAVIR
>                        seq2 MAaLAVvR

I don't know the answer about programs, but cannot contain myself.

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?

Admittedly if "." were used instead of "-" in Mansell's example, it would
satisfy me and probably him too, so my question is a bit off his point.

Joe Felsenstein, Dept. of Genetics, Univ. of Washington, Seattle, WA 98195
 Internet:         joe at genetics.washington.edu     (IP No.
 Bitnet/EARN:      felsenst at uwavm

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