GenBank（ジェンバンク）は、米国生物工学情報センター（NCBI; National Center for Biotechnology Information）が提供している、塩基配列データを蓄積・提供している世界的な公共の塩基配列データベースである。
目次
- 1 概要
- 2 登録と利用
- 3 関連項目
- 4 外部リンク
- 5 出典
概要[編集]
GenBankの塩基配列データには、注釈（アノテーション）が付されており、また対応するアミノ酸（タンパク質）配列の情報も持っている。
GenBankデータベースは、欧州分子生物学研究所（EMBL; European Molecular Biology Laboratory）傘下の欧州バイオインフォマティクス研究所（EBI; European Bioinformatics Institute）のEMBLデータライブラリ、および、日本DNAデータバンク（DDBJ; DNA Data Bank of Japan）と連携して、相互に塩基配列データを交換している。GenBankおよび共同活動をしているデータベースには、世界中の研究機関から10万種以上の生物から抽出された塩基配列が登録されている。
GenBank のデータは、指数関数的に増加しており（10ヵ月で2倍のペース）、2012年6月までに、8200万以上の塩基配列、約2870億個の核酸塩基（ヌクレオチド）のデータが登録された。GenBankデータベースには、世界各地の研究機関から直接データが登録されるほか、大規模な配列センターから、大量のデータが一括登録されることもある。
登録と利用[編集]
GenBankにインターネットを介して直接データを登録するには、BankItというWWWのフォームを使って登録する方法や、Sequinというスタンドアロンの登録用ソフトウェアを使って登録する方法などがある。GenBankに塩基配列のデータが登録されると、GenBankのスタッフがその配列に登録番号を振って、配列データの質の検査を行う。その後、登録されたデータが、実際にデータベースに反映される。
発現シーケンスタグ（EST; Expressed Sequence Tag）、STS（Sequence Tagged Site）、GSS（Genome Survey Sequence）、HTGS（High-Throughput Genome Sequence）のデータの一括登録は、通常、大規模な配列センターによって行われることが多い。完全な微生物ゲノム配列の場合は、GenBankに直接データを登録する方法が採られる。
Genbankデータベースのデータは、Entrezという検索エンジンで検索したり、FTPでダウンロードすることができる。
関連項目[編集]
- バイオインフォマティクス
- 分子生物学
- 欧州分子生物学研究所（EMBL）
- 欧州バイオインフォマティクス研究所（EBI）
- 日本DNAデータバンク（DDBJ）
外部リンク[編集]
- GenBank
- BankIt
- Sequin
- Emboss
出典[編集]
- This article contains material from the NCBI Handbook published by the NCBI, which, as a US government publication, is in the public domain [1].
GenBank
| Content |
| Description |
Nucleotide sequences for more than 300,000 organisms with supporting bibliographic and biological annotation. |
| Data types captured |
- Nucleotide sequence
- Protein sequence
|
| Organisms |
all |
| Contact |
| Research center |
NCBI |
| Primary citation |
PMID 21071399 |
| Release date |
1982; 31 years ago (1982) |
| Access |
| Data format |
|
| Website |
NCBI |
| Download URL |
ncbi ftp |
| Web service URL |
|
| Tools |
| Web |
BLAST |
| Standalone |
BLAST |
| Miscellaneous |
| License |
Public domain-US Government |
The GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations. This database is produced and maintained by the National Center for Biotechnology Information (NCBI) as part of the International Nucleotide Sequence Database Collaboration (INSDC). The National Center for Biotechnology Information is a part of the National Institutes of Health in the United States. GenBank and its collaborators receive sequences produced in laboratories throughout the world from more than 100,000 distinct organisms. In the more than 30 years since its establishment, GenBank has become the most important and most influential database for research in almost all biological fields, whose data are accessed and cited by millions of researchers around the world. GenBank continues to grow at an exponential rate, doubling every 18 months.[1][2] Release 194, produced in February 2013, contained over 150 billion nucleotide bases in more than 162 million sequences.[3] GenBank is built by direct submissions from individual laboratories, as well as from bulk submissions from large-scale sequencing centers.
Contents
- 1 Submissions
- 2 History
- 3 Growth
- 4 Incomplete Identifications
- 5 See also
- 6 References
- 7 External links
Submissions[edit]
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.
History[edit]
Walter Goad of the Theoretical Biology and Biophysics Group at Los Alamos National Laboratory and others established the Los Alamos Sequence Database in 1979, which culminated in 1982 with the creation of the public GenBank.[4] Funding was provided by the National Institutes of Health, the National Science Foundation, the Department of Energy, and the Department of Defense. LANL collaborated on GenBank with the firm Bolt, Beranek, and Newman, and by the end of 1983 more than 2,000 sequences were stored in it.
In the mid 1980s, the Intelligenetics bioinformatics company at Stanford University managed the GenBank project in collaboration with LANL.[5] 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.[6]
Genbank and EMBL: NucleotideSequences 1986/1987 Volumes I to VII.
Growth[edit]
Growth in GenBank base pairs, 1982 to 2007, on a semi-log scale
The GenBank release notes for release 162.0 (October 2007) state that "from 1982 to the present, the number of bases in GenBank has doubled approximately every 18 months".[3] [7]
As of 8 July 2013 (2013-07-08)[update], GenBank release 196.0 has 165,740,164 loci, 152,599,230,112 bases, from 165,740,164 reported sequences.[3]
The GenBank database includes additional data sets that are constructed mechanically from the main sequence data collection, and therefore are excluded from this count.
Top organisms in GenBank (Release 191)[8]
| Organism |
base pairs |
| Homo sapiens |
701016310774187000016,310,774,187 |
| Mus musculus |
70099974977889000009,974,977,889 |
| Rattus norvegicus |
70096521253272000006,521,253,272 |
| Bos taurus |
70095386258455000005,386,258,455 |
| Zea mays |
70095062731057000005,062,731,057 |
| Sus scrofa |
70094887861860000004,887,861,860 |
| Danio rerio |
70093120857462000003,120,857,462 |
| Strongylocentrotus purpuratus |
70091435236534000001,435,236,534 |
| Macaca mulatta |
70091256203101000001,256,203,101 |
| Oryza sativa Japonica Group |
70091255686573000001,255,686,573 |
| Nicotiana tabacum |
70091197357811000001,197,357,811 |
| Xenopus (Silurana) tropicalis |
70091249938611000001,249,938,611 |
| Drosophila melanogaster |
70091119965220000001,119,965,220 |
| Pan troglodytes |
70091008323292000001,008,323,292 |
| Arabidopsis thaliana |
70091144226616000001,144,226,616 |
| Canis lupus familiaris |
7008951238343000000951,238,343 |
| Vitis vinifera |
7008999010073000000999,010,073 |
| Gallus gallus |
7008899631338000000899,631,338 |
| Glycine max |
7008906638854000000906,638,854 |
| Triticum aestivum |
7008898689329000000898,689,329 |
Incomplete Identifications[edit]
Public databases, such as GenBank, which may be searched using the National Center for Biotechnology Information Basic Local Alignment Search Tool (NCBI BLAST), lack peer-reviewed sequences of type strains and sequences of non-type strains. On the other hand, while commercial databases potentially contain high-quality filtered sequence data, there are a limited number of reference sequences.
A paper released in the Journal of Clinical Microbiology[9] evaluated the 16S rRNA gene sequencing results analyzed with GenBank in conjunction with other freely available, quality-controlled, web-based public databases, such as the EzTaxon-e (http://eztaxon-e.ezbiocloud.net/) and the BIBI (http://pbil.univ-lyon1.fr/bibi/) databases. The results showed that analyses performed using GenBank combined with EzTaxon-e (kappa = 0.79) were more discriminative than using GenBank (kappa = 0.66) or other other databases alone.
See also[edit]
- Ensembl
- Human Protein Reference Database (HPRD)
- Sequence analysis
- UniProt
- List of sequenced eukaryotic genomes
- List of sequenced archeal genomes
- RefSeq — the Reference Sequence Database
- Geneious — includes a GenBank Submission Tool
References[edit]
- ^ Benson D, et al.; Karsch-Mizrachi, I.; Lipman, D. J.; Ostell, J.; Wheeler, D. L. (2008). "GenBank". Nucleic Acids Research 36 (Database): D25–D30. doi:10.1093/nar/gkm929. PMC 2238942. PMID 18073190.
- ^ Benson D, et al.; Karsch-Mizrachi, I.; Lipman, D. J.; Ostell, J.; Sayers, E. W. (2009). "GenBank". Nucleic Acids Research 37 (Database): D26–D31. doi:10.1093/nar/gkn723. PMC 2686462. PMID 18940867.
- ^ a b c "GenBank release notes". NCBI.
- ^ Hanson, Todd (2000-11-21). "Walter Goad, GenBank founder, dies". Newsbulletin: obituary. Los Alamos National Laboratory.
- ^ LANL GenBank History
- ^ Benton D (1990). "Recent changes in the GenBank On-line Service". Nucleic Acids Research 18 (6): 1517–1520. doi:10.1093/nar/18.6.1517. PMC 330520. PMID 2326192.
- ^ Benson, D. A.; Cavanaugh, M.; Clark, K.; Karsch-Mizrachi, I.; Lipman, D. J.; Ostell, J.; Sayers, E. W. (2012). "GenBank". Nucleic Acids Research 41 (Database issue): D36–D42. doi:10.1093/nar/gks1195. PMC 3531190. PMID 23193287. edit
- ^ Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (January 2011). "GenBank". Nucleic Acids Res. 39 (Database issue): D32–37. doi:10.1093/nar/gkq1079. PMC 3013681. PMID 21071399.
- ^ Kyung Sun Parka, Chang-Seok Kia, Cheol-In Kangb, Yae-Jean Kimc, Doo Ryeon Chungb, Kyong Ran Peckb, Jae-Hoon Songb and Nam Yong Lee (2012) J. Clin. Microbiol. May 2012 vol. 50 no. 5 1792-1795 Evaluation of the GenBank, EzTaxon, and BIBI Services for Molecular Identification of Clinical Blood Culture Isolates That Were Unidentifiable or Misidentified by Conventional Methods
- This article incorporates public domain material from the National Center for Biotechnology Information document "NCBI Handbook".
External links[edit]
- GenBank
- Example sequence record, for hemoglobin beta
- BankIt
- Sequin — a stand-alone software tool developed by the NCBI for submitting and updating entries to the GenBank sequence database.
- EMBOSS — free, open source software for molecular biology
- GenBank, RefSeq, TPA and UniProt: What's in a Name?
- GenBank File-Format Converter
|
Bioinformatics
|
|
| Databases |
- Sequence databases: GenBank, European Nucleotide Archive and DNA Data Bank of Japan
- Secondary databases: UniProt, database of protein sequences grouping together Swiss-Prot, TrEMBL and Protein Information Resource
- Other databases: Protein Data Bank, Ensembl and InterPro
- Specialised genomic databases: Saccharomyces Genome Database, FlyBase, WormBase, Arabidopsis Information Resource and Zebrafish Information Network
|
|
| Other |
- Algorithm: BLAST
- Server: ExPASy
|
|
| Institutions |
- European Bioinformatics Institute
- US Center for Biotechnology Information
- Swiss Institute of Bioinformatics
- Japanese Institute of Genetics
|
|
- List of biological databases
- Sequencing
- Sequence database
- Sequence alignment
- Molecular phylogenetics
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