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.
Department of Cellular and Developmental Biology
Department of Genetics / HHMI
robison at mito.harvard.edu