Nuclear Factor-DNA Binding Motifs

David Johnson Johnson at
Mon Nov 14 19:01:36 EST 1994

   Is there a database/search program available that can search for
nuclear factor binding motifs in a given DNA sequence?  Note that this is
*not* the same as searching the eukaryotic promoter database (epd) with
Blast, contrary to recent "answers" given in this newsgroup, because
Blast/epd searches for homologous sequences in other promoters.  For
example, Blast/epd would yield many matches if a (query) DNA sequence
includes an NF-kB (nuclear factor) binding motif because many eukaryotic
promoters contain NF-kB sites.  
   Instead, it would be useful to be able to submit a DNA sequence for
identification of binding motifs (putative binding sites).  For example,
an NF-kB binding motif would be identified in a DNA sequence. 
   The mbcrr computer at the Dana-Farber Cancer Institute in Boston had
such a program several years back.  This program also provided a journal
reference for the binding motif.  

Chance favors the prepared mind- do you feel lucky, punk?

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