Motif search help page

This page provides the overview of the Motif search service on GenomeNet. Each link shows the detailed description for the service as well as useful information such as reference to the original web site of the database supported on our server.

We supports serveral motif databases;

PROSITE

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.

PubMed: 11752303

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).

PubMed: 96039003

BLOCKS

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.

PubMed: 10592233

Henikoff S., Henikoff J.G. Pietrokovski S.
Blocks+: A non-redundant database of protein alignment blocks dervied from multiple compilations
Bioinformatics 15:471-479 (1999)

PubMed: 10383472

ProDom

Corpet F., Gouzy J., Kahn D.
Recent improvements of the ProDom database of protein domain families.
Nucleic Acids Res. 27:263-267 (1999)

PubMed: 99063708.

Sonnhammer E.L., Kahn D.
Modular arrangement of proteins as inferred from analysis of homology.
Protein Sci. 3:482-492 (1994)

PubMed: 94290324

PRINTS

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.

PubMed: 11752304

Pfam

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.

PubMed: 11752314

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 annotations. The results will also be presented graphically, and especially, where available, 3D structures of the found motifs can be examined by RasMol 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.

Motif Libraries	Search Engines	Developpers of Engines	Search Algorithm
PROSITE PATTERN	Motiffind	ICR, Kyoto Univ.
PROSITE PROFILE	Profilefind	ICR, Kyoto Univ.	Dynamic Programing method
BLOCKS	BLIMPS	Fred Hutchinson Cancer Research Center
ProDom	Blastp	NCBI	BLAST2 (Gapped BLAST)
PRINTS	BLIMPS	Fred Hutchinson Cancer Research Center
Pfam	Hmmscan (HMMER)	Howard Hughes Medical Institute	Profile Hidden Markov Model

Given a profile which was generated from the multiple sequence alignment, or, retrieved from motif library such as PROSITE or Pfam, 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.

Profile Format	Search Engines	Search Algorithm
PROSITE	Profilefind	Dynamic Programing method
Pfam-hmmer	Hmmscan	Profile Hidden Markov Model

Given a profile, protein sequence databases on GenomeNet service are retrieved to find out the protein families that have the same motif. The profile, either in PROSITE or Pfam format, could be calculated in our service from the multiple sequence alignment or retrieved from motif library such as PROSITE or Pfam. The Pfsearch program is used to retrieve with PROSITE format profile and Hmmsearch is used for Pfam format one. Target sequence libraries are Swiss-Prot, PDBSTR, PIR, PRF and Genes.

This allows you to search protein sequence libraries with your patterns. Target sequence libraries are Swiss-Prot, PDBSTR, PIR, PRF and Genes. Sequence pattern must be specified in the PROSITE pattern format, namely;

Each residue must be separated with - (minus sign).
x represents any amino acids.
[DE] means either D or E.
{FWY} means any amino acids except for F, W and Y
A(2,3) means that A appears 2 to 3 times consecutively.
The pattern string must be terminated with . (period).

For example, C-x-{C}-[DN]-x(2)-C-x(5)-C-C.

Two type of profile data, either in PROSITE or Pfam format, are calculated from the multiple alignment sequences. using PFMake or HMMBuild, respectively.

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 are shown.

RasMol is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules.
You can also find Chime, a free plug-in of web browser running on both Windows and Macintosh available from MDL.