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The UniProt database is an example of a protein sequence database. As of 2013 it contained over 40 million sequences and is growing at an exponential rate. [1] Historically, sequences were published in paper form, but as the number of sequences grew, this storage method became unsustainable.
The GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations. It is produced and maintained by the National Center for Biotechnology Information (NCBI; a part of the National Institutes of Health in the United States) as part of the International Nucleotide Sequence Database Collaboration (INSDC).
3D structure protein databases, Protein sequence databases MobiDB: Database of intrinsically disordered and mobile proteins: John Moult, Christine Orengo, Predrag Radivojac University of Padua: Italian Government database of intrinsic protein disorder annotation 3D structure protein databases, Protein sequence databases ModBase
USGENE provides searchable access to all available peptide and nucleotide sequences from the published applications and issued patents of the United States Patent and Trademark Office (USPTO). [8] USGENE can be searched directly via the SequenceBase Research Portal [ 9 ] or via STN International [ 10 ] [ 11 ] by FIZ Karlsruhe .
Using the typical values for assessing the significance is called the lookup table method; it is not accurate. The expect score E of a database match is the number of times that an unrelated database sequence would obtain a score S higher than x by chance. The expectation E obtained in a search for a database of D sequences is given by
Iterative sequence search scheme of HHblits. Modern sensitive methods for protein search utilize sequence profiles. They may be used to compare a sequence to a profile, or in more advanced cases such as HH-suite, to match among profiles. [2] [6] [7] [8] Profiles and alignments are themselves derived from matches, using for example PSI-BLAST or ...
The Reference Sequence (RefSeq) database [1] is an open access, annotated and curated collection of publicly available nucleotide sequences (DNA, RNA) and their protein products. RefSeq was introduced in 2000.
The International Nucleotide Sequence Database Collaboration (INSDC) consists of a joint effort to collect and disseminate databases containing DNA and RNA sequences. [1] It involves the following computerized databases: NIG's DNA Data Bank of Japan (), NCBI's GenBank and the EMBL-EBI's European Nucleotide Archive ().