> Hi everybody,
> This may be a simple thing to do, but do not know how to do it.
> I have a set of eight DNA sequences, out of which four are part of promoter
> sequences and the other four are non-promoters. I which to find which four
> are promoters and the nonpromoters.
> Is there any server or software which can do this fast.? Can I use any search
> program to find the promoter sequence?
If you are using a Mac there is the freeware MacTargsearch. With it you
can define weights to each nucleotide, spacing, etc. It then searches your
sequence database an returns a list of sequences that fit the criteria,
scoring each with a number. It's a very good program. I've included a
snippet that comes with the program. I don't know where it is posted
though. I can forward a copy if you like.
MacTargsearch is a compiled Microsoft BASIC (b) program created by James A.
Goodrich, William R. McClure, and Michael L. Schwartz in 1989 at the Department
of Biological Sciences, Carnegie Mellon University. The program allows one
to search a sequence of DNA base pairs for the occurrence of sites with sequence
similarity to a target site. A Macintosh computer with at least 1MB of RAM
and a printer are required to run the program. Any questions or comments
can be addressed to Jim Goodrich at Carnegie Mellon University, 4400 Fifth
Avenue, Pittsburgh, Pa. 15213 or (412) 268-3201.
BMBCB, Northwestern University
Evanston, IL USA