Nuclear Factor-DNA Binding Motifs
Johnson at biomed.yale.edu
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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