IUBio Biosequences .. Software .. Molbio soft .. Network News .. FTP

QUESTION_ON_PILEUP

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
defaults.  

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



More information about the Info-gcg mailing list

Send comments to us at biosci-help [At] net.bio.net