- Use Entrez to search nucleotide or protein sequences, protein structures or genomes.
- PIR is also available at the Martinsrieder Institut für Proteinsequenzen (MIPS), including some search facilities like FASTA, and at the Georgetown University, including some fancy search utilities.
- The EMBL offers SRS which is a sequence retrieval system which indexes all of the major databases.
- The EBI offers various search programs and the PredictProtein home page.
- Ensembl, the database of the human genome.
- ExPASy server at Geneva with and several tools
- John Hopkins Prot-Web server with
and several tools
- OWL, a non-redundant protein sequence database
- NRL-3D, which contains all protein sequences for which the 3D structure is known
- REBASE, which contains all known restriction enzymes
- TIGR (The Institute for Genomic Research)
- GenQuest server
- BLAST searches at the NCBI (National Center of Biotechnology Information).
- BLAST searches at EMBnet-CH/SIB/CSCS (Switzerland) using the Expasy interface
- The whole FASTA suite of programs
- FASTA3 will soon be replaced by FASTA33
- General sequence analysis
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