IUBio

Multiple sequence outputs???

Rodrigo Lopez rodrigol at biomaster.uio.no
Thu May 26 05:11:47 EST 1994


In article <1994May25.103412.1 at omrf.uokhsc.edu>, frank at omrf.uokhsc.edu writes:
|> We have aligned two groups of sequences with a short overlap using 
|> the fragmetn assembly software.  The total consensus length is about
|> 500 bp.  The second group of sequences is offset about 300 bp from
|> position 1.
|> 
|> Now we would like to get a printout with identical nucleotides to 
|> the consensus shown as a "-" and differences as the actual base.
|> We have tried to use pileup but it gives a completely different
|> and very poor alignment. Can you make a data file for the program
|> PRETTY that includes offset information for each sequence?  Are 
|> there alternate strategies to see these differences?
|> 
|> Thanks,
|> Bart Frank 
|> 


What you want exists as part of the EGCG package distributed
by GCG in their tapes and CDROMs. The program is called GelPicture
and will generate a file which displays the alignment and consensus
for each contig in a FAS project.

R:)


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