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
