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Pileup Help!

Mukul Ranjan ranjan at helix.nih.gov
Sun Apr 23 12:02:18 EST 1995


Hi Netters

   I have a somewhat complicated question concerning the alignment of
multiple DNA sequences using Pileup. The problem was encountered while
trying to determine the sequence similarities of a rapidly expanding gene
family. There is some confusion in the database since the same gene has
often been independently cloned and given different names, consequently
having an alignment and a dendrogram would immediately identify the
problem sequences.

   Essentially I have a file containing 192 sequence names. I have
manually taken out those sequences that are greater than 7000 bp., and
attempted to do a pileup with the command:

pileup @ptp.str4 -MAXS=7000

However the program comes back with the message: Error greater than 0 gap
insertions.

   I apologize if this is an obvious question that has previously been answered.

   Thanks.

Mukul Ranjan
________________________________________________________________________
ranjan at helix.nih.gov
NINDS,NIH
Bldg36/5D05 
Tel  (301) 594-2866(o)
Fax (301) 496-0899(o)

-- 
Mukul Ranjan
ranjan at helix.nih.gov



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