Sequence alignments -- where to chop?

Panhead McNipper wblank at gpu.srv.ualberta.ca
Tue Apr 16 16:41:58 EST 1996

Just trying to figure out the most "appropriate" course of action...

I want to place 16S sequences obtained in our lab on a tree with closely
related sequences from GenBank, but one of them isn't complete (e.g. a
string of about 60 Ns between nucleotides 940-1000).  Should I:
    A) go ahead anyway?
    B) cut the offending region out of all the sequences in the alignment?
    C) leave the incomplete sequence out entirely?
I plan to go ahead with option B (60 bases out of 1400-some isn't _too_ much
info lost, is it?) but want to know how others treat this sort of thing.

Thanks much
"The company of the future has only two employees:
 a man
 and a dog.
 The job of the man is to feed the dog.
 The job of the dog is to keep the man away from the computer." -- Chico

It's all much appreciated.  Out!

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