In October 2024, GenBank contained 34 trillion base pairs from over 4.7 billion nucleotide sequences and more than 580,000 formally described species.[2][3]
GenBank is built by direct submissions from individual laboratories, as well as from bulk submissions from large-scale sequencing centers.
Submissions
Only original sequences can be submitted to GenBank. Direct submissions are made to GenBank using BankIt, which is a Web-based form, or the stand-alone submission program, Sequin. Upon receipt of a sequence submission, the GenBank staff examines the originality of the data and assigns an accession number to the sequence and performs quality assurance checks. The submissions are then released to the public database, where the entries are retrievable by Entrez or downloadable by FTP. Bulk submissions of Expressed Sequence Tag (EST), Sequence-tagged site (STS), Genome Survey Sequence (GSS), and High-Throughput Genome Sequence (HTGS) data are most often submitted by large-scale sequencing centers. The GenBank direct submissions group also processes complete microbial genome sequences.[6][7]
In the mid-1980s, the Intelligenetics bioinformatics company at Stanford University managed the GenBank project in collaboration with LANL.[9] As one of the earliest bioinformatics community projects on the Internet, the GenBank project started BIOSCI/Bionet news groups for promoting open access communications among bioscientists. During 1989 to 1992, the GenBank project transitioned to the newly created National Center for Biotechnology Information (NCBI).[10]
Genbank and EMBL: NucleotideSequences 1986/1987 Volumes I to VII.CD-ROM of Genbank v100
Growth
Growth in GenBank base pairs, 1982 to 2018, on a semi-log scale
The GenBank release notes for release 250.0 (June 2022) state that "from 1982 to the present, the number of bases in GenBank has doubled approximately every 18 months".[11][12] As of 15 June 2022, GenBank release 250.0 has over 239 million loci, 1,39 trillion nucleotide bases, from 239 million reported sequences.[11]
The GenBank database includes additional data sets that are constructed mechanically from the main sequence data collection, and therefore are excluded from this count.
An analysis of Genbank and other services for the molecular identification of clinical blood culture isolates using 16S rRNA sequences[13] showed that such analyses were more discriminative when GenBank was combined with other services such as EzTaxon-e[14] and the BIBI[15] databases.
GenBank may contain sequences wrongly assigned to a particular species, because the initial identification of the organism was wrong. A recent study showed that 75% of mitochondrial Cytochrome c oxidase subunit I sequences were wrongly assigned to the fish Nemipterus mesoprion resulting from continued usage of sequences of initially misidentified individuals.[16] The authors provide recommendations how to avoid further distribution of publicly available sequences with incorrect scientific names.
Numerous published manuscripts have identified erroneous sequences on GenBank.[17][18][19] These are not only incorrect species assignments (which can have different causes) but also include chimeras and accession records with sequencing errors. A recent manuscript on the quality of all Cytochrome b records of birds further showed that 45% of the identified erroneous records lack a voucher specimen that prevents a reassessment of the species identification.[20]
Another problem is that sequence records are often submitted as anonymous sequences without species names (e.g. as "Pelomedusa sp. A CK-2014" because the species are either unknown or withheld for publication purposes. However, even after the species have been identified or published, these sequence records are not updated and thus may cause ongoing confusion.[21]
^The download page at UCSC says "NCBI places no restrictions on the use or distribution of the GenBank data. However, some submitters may claim patent, copyright, or other intellectual property rights in all or a portion of the data they have submitted. NCBI is not in a position to assess the validity of such claims, and therefore cannot provide comment or unrestricted permission concerning the use, copying, or distribution of the information contained in GenBank."
^Eric W Sayers; Mark Cavanaugh; Karen Clark; Kim D Pruitt; Conrad L Schoch; Stephen T Sherry; Ilene Karsch-Mizrachi (7 January 2022). "GenBank". Nucleic Acids Archive. 50 (D1): D161 –D164. doi:10.1093/nar/gkab1135. PMC8690257. PMID34850943.
