Peter Stockwell peter at sanger.otago.ac.nz
Sun Apr 30 15:55:11 EST 1995

smg at vax8.cfsan.fda.gov wrote:
> 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
> defaults.  

There have been discussions of this problem in other bionet SW groups:

The problem basically arises from the use of a version of the Clustal 
algorithm in PILEUP and its effects at the ends of sequences.  The MAP
program of Xiaoqiu Huang (Cabios (1994), 10, 227) provides a solution to
this problem, although preparation of the sequence data and running the
program do not conform to GCG's user interface or convenience.

Huang's program is freely available (see the reference) and is written in
C - I have had no problems in compiling it.

Peter A. Stockwell

> 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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