WWW seq alignment site with "jumbling" test of significance?
Gregg B Wells
wellsg at mail.med.upenn.edu
Tue Jan 9 22:13:36 EST 1996
Neil Clarke (Neil.Clarke at qmail.bs.jhu.edu) wrote:
: Anyone know of a WWW site that does an alignment between two protein
: sequences with the option of rerunning the alignement using a randomized
: ("jumbled") sequence? as a test of significance? Having just given a
: lecture on sequence analysis during which I extolled the virtues of the
: Web, I was surprised to find that I couldn't find a good old-fashioned
: Needleman-Wunsch type program out there. Lots of local homology search
: algorithms and dynamic programming algorithms for database searching, but
: no 'optimal' sequence alignment stuff. Help, please!
The Smith-Waterman algorithm can be used at the GenQuest site from Oak
Ridge National Laboratory for searching protein and DNA sequences. Here
is the email address for more information:
GENQUEST E-MAIL SERVER USER MANUAL
GenQuest can be accessed by sending e-mail to: Q at ornl.gov
Messages to GENQUEST begin with a set of keywords which specify the
be used in the search. Two key words are mandatory: TYPE and SEQ. The
are optional or have default settings. GENQUEST is case insensitive.
EXAMPLE of a typical query:
METHOD SW -g 13
This example translates the given DNA sequence in 6 frames and searches
SwissProt, using Smith-Waterman with gap penalty of 13, PAM120 matrix, and
showing top 50 matches and top 20 alignments.
Department of Pathology
University of Pennsylvania
email: wells at athens.dental.upenn.edu
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