smg at vax8.cfsan.fda.gov smg at vax8.cfsan.fda.gov
Fri Apr 28 08:34:39 EST 1995

I am trying to use PileUp to compare three sequences.  They all include the
same coding sequence, but have different amounts of flanking sequence.  When I
use PileUp and restrict it to just the coding region of each sequence I get a
perfect alignment, but when I run it with the complete sequences the
"alignment" is terrible.  There is essentially no match between the three,
including the fact that the program does -not- align the three identical coding
regions.  What am I doing wrong?  By the way - I am using all the program

I a related question - I would like to align another set of three sequences,    
but one of them was put in the data base as the non-coding strand.  Can I get   
PileUp to use the complement of this sequence?

Thanks for your help.

Steve Gendel
Biotechnology Studies
Center for Food Safety and Applied Nutrition, FDA
smg at vax8.cfsan.fda.gov

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