We supports serveral motif databases;
Falquet L., Pagni M., Bucher P., Hulo N., Sigrist C.J, Hofmann K. and Bairoch A.
"The PROSITE database, its status in 2002"
Nucl. Acids Res. 30(1):235-238, 2002.
Bucher P., Bairoch A.
A generalized profile syntax for biomolecular sequences motifs and its function in automatic sequence interpretation
In "ISMB-94; Proceedings 2nd International Conference on Intelligent Systems for Molecular Biology."
(Altman R., Brutlag D., Karp P., Lathrop R., Searls D., Eds.), pp53-61, AAAIPress, Menlo Park, (1994).
J.G. Henikoff, E.A. Greene, S. Pietrokovski and S. Henikoff
"Increased coverage of protein families with the blocks database servers"
Nucl. Acids Res. 28(1):228-230, 2000.
Corpet F., Gouzy J., Kahn D.
Recent improvements of the ProDom database of protein domain families.
Nucleic Acids Res. 27:263-267 (1999)
Sonnhammer E.L., Kahn D.
Modular arrangement of proteins as inferred from analysis of homology.
Protein Sci. 3:482-492 (1994)
Attwood, T.K., Blythe, M., Flower, D.R., Gaulton, A., Mabey, J.E., Maudling, N., McGregor, L., Mitchell, A., Moulton, G., Paine, K. and Scordis, P.
"PRINTS and PRINTS-S shed light on protein ancestry."
Nucl. Acids Res. 30(1):239-241, 2002.
Bateman A., Birney E., Cerruti L., Durbin R., Etwiller L., Eddy SR.,
Griffiths-Jones S., Howe K.L., Marshall M. and Sonnhammer E.L.
"The Pfam Protein Families Database"
Nucl. Acids Res. 30(1):276-280, 2002.
as well as
· user defined profile library
(may contain multiple profile data)
This server not only finds out sequence motifs in your query sequence, but also provides
functional and genomic information of the found motifs using DBGET and LinkDB as the hyperlinked
The results will also be presented graphically, and especially, where available, 3D structures of the found motifs
can be examined by
program when the hits are found in PROSITE database.
(You need to install RasMol program beforehand. See instructions to setup RasMol
Click each Motif library database name colomun to see detailed explanation.
Given a profile which was generated
from the multiple sequence alignment
retrieved from motif library such as PROSITE
you can align a protein sequence with the profile.
The procedure is similar to the one to search against the motif library database, however, you should provide
a name of the file containing profile matrix instead of the database names.
||Dynamic Programing method
||Profile Hidden Markov Model
Two type of profile data, either in PROSITE
or Pfam format
, are calculated from the multiple alignment sequences.
You can align your (new) sequence against this generated profile continuously, or save the obtained profile on your local computer to use to search against sequence databases. Additional explanations