In article <3265 at emoryu1.cc.emory.edu> bcresas at emoryu1.cc.emory.edu writes:
>Are there other protein motif-type databases available to search besides Prosite?
>>>Scott A. Sammons
I'm including some information about the Blocks database at the end of
this article.
To find more information - point your gopher client at merlot.welch.jhu.edu
- if using Unix or Vax client just type:
gopher merlot.welch.jhu.edu
Select the following:
--> 13. Search Databases at Hopkins (Vectors, Promoters, NRL-3D, EST, OMIM../
--> 9. Seqanalref - Sequence Analysis Bibliographic Reference Data Ban.. <?>
Now search for motif*
+---Seqanalref - Sequence Analysis Bibliographic Reference Data Bank----+
| _____________ |
| Words to search for | motif* | |
| ------------- |
| [Cancel ^G] [Accept - Enter] |
| |
+-----------------------------------------------------------------------+
And you'll get 85 entries - a sample entry is as follows:
------------
ID GRIM8801
RM 88252899
RA Gribskov M., Homyak M., Edenfield J., Eisenberg D.;
RT "Profile scanning for three-dimensional structural patterns in protein
RT sequences.";
RL Comput. Appl. Biosci. 4:61-66(1988).
KW PROTEIN; MATRIX-PROFILE.
Profile analysis measures the similarity between a target sequence and a
group of aligned sequences (the probe). The probe sequences are used to
produce a position-specific scoring table (the profile) that can be aligned
with any sequence (the target) using standard dynamic programming methods.
We are developing a library of profiles, each describing a different
structural motif. This allows any target sequence to be rapidly scanned for
the presence of structural motifs. Levels of significance for the
comparison of target sequences with the profile are determined in advance,
permitting an objective decision to be made as to whether a protein is
likely to possess a structural motif.
--------------
You might ant to narrow your search down a little bit - so try
+---Seqanalref - Sequence Analysis Bibliographic Reference Data Bank----+
| ________________________ |
| Words to search for | motif* and database | |
| ------------------------ |
| [Cancel ^G] [Accept - Enter] |
| |
+-----------------------------------------------------------------------+
Will yield 21 entries and the following will fill in the gap and yield
13 entries.
+---Seqanalref - Sequence Analysis Bibliographic Reference Data Bank----+
| _____________________________ |
| Words to search for | motif* and data and bank | |
| ----------------------------- |
| [Cancel ^G] [Accept - Enter] |
| |
+-----------------------------------------------------------------------+
You might also try searching the Gentools Bibliographys:
--> 14. Search the GenTools Bibliography <?>
If you've never heard of gopher don't worry it's free and on the net.
Write me a note if you'd like info on hpw to get started.
Best of luck,
Dan Jacobson
danj at welchgate.welch.jhu.edu
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