IUBio

nucleotide consensus search

Nathan Weyand Nate_Weyand at HLTHSCI.MED.UTAH.EDU
Tue Jun 24 18:03:04 EST 1997


Hi all,
  I have a question about searching for a short nucleotide consensus 
sequence.  The sequence is only 10 nucleotides long and represents a 
protein binding site with in a promoter.  Specifically, I want to search 
the E. coli genome for this consensus sequence.  I have tried a fasta 
and blastn search in GCG without success.  Is it possible to search for 
such a short consensus in GCG databases such as - [nr n Non-redundant 
GenBank+EMBL+DDBJ+PDB sequences]?  Does anybody have any suggestions on 
what settings I need to adjust for a successful search or whether web 
resources exist that can be used for my problem?

Any suggestions would be welcome! Thanks in advance for any help you can 
offer.  I will post a summary of advice I get that leads me in the 
right direction.

sincerely,

Nate Weyand
email:  Nate_Weyand at hlthsci.med.utah.edu



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