Protein Sequences

Database

• Swiss-Prot (Sequence Database)
• PIR (Protein Identification Resource Database)
• Breast Cancer Gene Database
• EC Enzyme (Enzyme Database)
• ENTREZ (Protein and Nucleotide Database)
• G-Protein Coupled Receptor Database
• Genbank
• Genome Web
• GDB (Genome Database)
• OWL (Composite Protein Sequence Database)
• p53 database
• Protein-Disease Database
• SWISS-2DPAGE
• SYSTERS Cluster Set
• Tumor Gene Database

Sequence Analysis/Comparison

• BLAST / PSI-BLAST
• GRAIL™
• GenQuest
• ALIGN
• BCM Search Launcher
• BEAUTY
• Bioinformation Search Center
• BioSCAN
• BLOCKS WWW Server
• EMBnet-CH BLAST2
• ExPASy Molecular Biology Server
• FASTA
• Hydrophobicity Profile
• Protein Hydrophilicity/Hydrophobicity Search and Comparison Server
• GAIA
• pimaII
• PROSITE (Dictionary of protein sites and patterns)
• SBASE 5 (Annotated protein domain sequences)
• SSEARCH
• Zinfo

Multiple Sequence Alignment

• CINEMA
• CLUSTAL W
• CypData
• ITERALIGN
• MEME
• Multiple Sequence Alignment Interface
• BCM Search Launcher

Membrane Proteins

• MEMSAT
• SOSUI
• TMpred
• TMHMM
• TMAP

Signal Prediction

• DictyOGlyc (GlcNAc O-glycosylation sites in Dictyostelium discoideum proteins)
• NetOGlyc (mucin type GalNAc O-glycosylation sites in mammalian proteins)
• NetPicoRNA (posttranslational cleavage sites by picornaviral proteases)
• PSORT WWW Server (cellular localization)
• SignalP (signal peptide cleavage sites)

Domain Parsing

• DOMO
• ProDom
• SMART

Protein Families

• Molecular Sequence Megaclassification
• Pfam (Collection of Protein Domain Families)
• ProClass Database
• Protein Families Database

Phylogenies

• PASSML
• PHYLIP

Utilities

• Biology WorkBench
• JaMBW
• READSEQ