Table 1 Useful tools and resources for protein family, domain and motif analysis

Blocks

Database of protein alignment blocks

http://blocks.fhcrc.org

[19]

CDD

Conserved domain database

http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml

[47]

CluSTr

Clusters of SWISS-PROT and TrEMBL proteins

http://www.ebi.ac.uk/clustr/

[34]

DOMO

Protein-domain database based on sequence alignments

http://www.infobiogen.fr/services/domo/

[24]

InterPro

Integrated documentation resource for protein families, domains and functional sites

http://www.ebi.ac.uk/interpro/

[49]

IProClass

Integrated protein classification database

http://pir.georgetown.edu/iproclass/

[45]

MetaFam

Database of protein family information

http://metafam.ahc.umn.edu/

[43]

Pfam

Collection of multiple sequence alignments and hidden Markov models

http://www.sanger.ac.uk/Software/Pfam/

[13]

PIR

Protein Information Resource

http://pir.georgetown.edu/

[4]

PIR-ALN

Curated database of protein sequence alignments

http://pir.georgetown.edu/pirwww/dbinfo/piraln.html

[26]

PRINTS-S

Compendium of protein fingerprints

http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/

[11]

ProClass

Non-redundant protein database organized by family relationships

http://pir.georgetown.edu/gfserver/proclass.html

[28]

ProDom

Automatic compilation of homologous domains

http://prodes.toulouse.inra.fr/prodom/doc/prodom.html

[21]

PROSITE

Database of patterns and profiles describing protein families and domains

http://www.expasy.ch/prosite/

[9]

ProtoMap

Automatic hierarchical classification of SWISS-PROT proteins

http://www.protomap.cs.huji.ac.il/

[30]

SBASE

Curated protein domain library based on sequence clustering

http://www3.icgeb.trieste.it/~sbasesrv/

[51]

SMART

Simple Modular Architecture Research Tool - a collection of protein families and domains

http://smart.embl-heidelberg.de/

[15]

SWISS-PROT and TrEMBL

Protein sequence databases

http://www.ebi.ac.uk/swissprot/ or http://www.expasy.org/sprot/

[2]

SYSTERS

Systematic re-searching method for sequence searching and clustering

http://systers.molgen.mpg.de/

[32]

TIGRFAMs

Protein families based on hidden Markov models

http://www.tigr.org/TIGRFAMs/

[17]