Table 1.

Publicly available tools and databases for bioinformatic analysis

Name URL	Function (Refer to the manual of each tool for more details)
Algorithms
ID Mapping www.uniprot.org/?tab=mapping	Map identifiers to or from UniProtKB.
PICR www.ebi.ac.uk/Tools/picr/	Map identifiers based on sequence identity.
UCSC Genome Browser genome.ucsc.edu	Visualize the location of genes within genome.
ProtParam web.expasy.org/protparam/	Compute various physiochemical parameters for a given protein.
PROSITE prosite.expasy.org	Determine protein domains and families.
DAVID Bioinformatics Resources david.abcc.ncifcrf.gov	Annotate large list of genes based on gene ontology.
GENE ONTOLOGY (GO) Tools go.princeton.edu	GO Term Finder and GO Term Mapper. Find significant GO terms shared by a list of genes.
Clover zlab.bu.edu/clover/	Identify overrepresented functional sites within a set of DNA sequences.
Cytoscape www.cytoscape.org	Analyze and visualize complex protein-protein interaction networks.
Databases
Database of Interacting Proteins dip.doe-mbi.ucla.edu/	Database for experimentally determined interactions between proteins.
Ensembl www.ensembl.org	Genome database for vertebrates and other eukaryotic species.
InterPro www.ebi.ac.uk/interpro/	Database for protein families, domains, regions and sites.
KEGG PATHWAY www.genome.jp/kegg/pathway.html	Database of molecular interaction and reaction networks.
MotifMap motifmap.ics.uci.edu	Comprehensive maps of candidate regulatory elements encoded in the genomes of model species.