How can I search for a motif?

Keith Robison robison at mito.harvard.edu
Wed Oct 19 16:56:51 EST 1994

Castor Menendez (menendez at mibm.ruf.uni-freiburg.de) wrote:
: Dear netters,
:              Does anybody knows how can I perform a database search 
:              for a particular motif ?

:              I would like to evaluate the ocurrence of a particular 
:              string of aminoacids (just 9 and looking something like 
:              ExxYCxxCxDC, where x means any a.a.). 

:              I tried already with one server and I got a message saying 
:              that my sequence was too short for a search. Does anybody knows 
:              which server could handle this search?.

:              All suggestions and details will be welcomed.

You can get BLAST to accept this if you configure the parameters correctly.
The key is to use a different substitution matrix.  There is an
"identity" matrix which penalizes mismatches to the hilt, or you
might try one of the short-distance matrices (such as PAM10 or

I don't offhand know of a server which will accept arbitrary regular
expressions and search them.  The problem is that this type of 
search can be a bear on the host computer.  You might try running such
a search locally using either a commercial package or J.Tisdall's 
DNA Workbench, which is especially good for pattern searches and should
run on just about any computer.

Keith Robison
Harvard University
Department of Cellular and Developmental Biology
Department of Genetics / HHMI

robison at mito.harvard.edu 

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