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The National Center for Biotechnology Information (NCBI) is part of the (NLM), a branch of the National Institutes of Health (NIH). It is approved and funded by the government of the United States. The NCBI is located in Bethesda, Maryland, and was founded in 1988 through legislation sponsored by US Congressman Claude Pepper.
In the field of bioinformatics, a sequence database is a type of biological database that is composed of a large collection of computerized ("digital") nucleic acid sequences, protein sequences, or other polymer sequences stored on a computer. 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. Historically, sequences were published in paper form, but as the number of sequences grew, this storage method became unsustainable.
In genetics, an expressed sequence tag (EST) is a short sub-sequence of a cDNA sequence. ESTs may be used to identify gene transcripts, and were instrumental in gene discovery and in gene-sequence determination. The identification of ESTs has proceeded rapidly, with approximately 74.2 million ESTs now available in public databases. EST approaches have largely been superseded by whole genome and transcriptome sequencing and metagenome sequencing.
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 as part of the International Nucleotide Sequence Database Collaboration (INSDC).
UniProt is a freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived from the research literature. It is maintained by the UniProt consortium, which consists of several European bioinformatics organisations and a foundation from Washington, DC, USA.
The European Bioinformatics Institute (EMBL-EBI) is an intergovernmental organization (IGO) which, as part of the European Molecular Biology Laboratory (EMBL) family, focuses on research and services in bioinformatics. It is located on the Wellcome Genome Campus in Hinxton near Cambridge, and employs over 600 full-time equivalent (FTE) staff.
InterPro is a database of protein families, protein domains and functional sites in which identifiable features found in known proteins can be applied to new protein sequences in order to functionally characterise them.
David J. Lipman is an American biologist who from 1989 to 2017 was the director of the National Center for Biotechnology Information (NCBI) at the National Institutes of Health. NCBI is the home of GenBank, the U.S. node of the International Sequence Database Consortium, and PubMed, one of the most heavily used sites in the world for the search and retrieval of biomedical information. Lipman is one of the original authors of the BLAST sequence alignment program, and a respected figure in bioinformatics. In 2017, he left NCBI and became Chief Science Officer at Impossible Foods.
The DNA Data Bank of Japan (DDBJ) is a biological database that collects DNA sequences. It is located at the National Institute of Genetics (NIG) in the Shizuoka prefecture of Japan. It is also a member of the International Nucleotide Sequence Database Collaboration or INSDC. It exchanges its data with European Molecular Biology Laboratory at the European Bioinformatics Institute and with GenBank at the National Center for Biotechnology Information on a daily basis. Thus these three databanks contain the same data at any given time.
The Genomic Standards Consortium (GSC) is an initiative working towards richer descriptions of our collection of genomes, metagenomes and marker genes. Established in September 2005, this international community includes representatives from a range of major sequencing and bioinformatics centres and research institutions. The goal of the GSC is to promote mechanisms for standardizing the description of (meta)genomes, including the exchange and integration of (meta)genomic data. The number and pace of genomic and metagenomic sequencing projects will only increase as the use of ultra-high-throughput methods becomes common place and standards are vital to scientific progress and data sharing.
The Reference Sequence (RefSeq) database is an open access, annotated and curated collection of publicly available nucleotide sequences and their protein products. RefSeq was introduced in 2000. This database is built by National Center for Biotechnology Information (NCBI), and, unlike GenBank, provides only a single record for each natural biological molecule for major organisms ranging from viruses to bacteria to eukaryotes.
UGENE is computer software for bioinformatics. It works on personal computer operating systems such as Windows, macOS, or Linux. It is released as free and open-source software, under a GNU General Public License (GPL) version 2.
KIAA0895 is a protein that in Homo sapiens is encoded by the KIAA0895 gene. The gene encodes a protein commonly known as the KIAA0895 protein. Its aliases include hypothetical protein LOC23366, OTTHUMP00000206979, OTTHUMP00000206980, 9530077C05Rik, and 1110003N12Rik. It is located at 7p14.2.
The Sequence Read Archive is a bioinformatics database that provides a public repository for DNA sequencing data, especially the "short reads" generated by high-throughput sequencing, which are typically less than 1,000 base pairs in length. The archive is part of the International Nucleotide Sequence Database Collaboration (INSDC), and run as a collaboration between the NCBI, the European Bioinformatics Institute (EBI), and the DNA Data Bank of Japan (DDBJ).
The European Nucleotide Archive (ENA) is a repository providing free and unrestricted access to annotated DNA and RNA sequences. It also stores complementary information such as experimental procedures, details of sequence assembly and other metadata related to sequencing projects. The archive is composed of three main databases: the Sequence Read Archive, the Trace Archive and the EMBL Nucleotide Sequence Database. The ENA is produced and maintained by the European Bioinformatics Institute and is a member of the International Nucleotide Sequence Database Collaboration (INSDC) along with the DNA Data Bank of Japan and GenBank.
Zinc finger protein 684 is a protein that in humans is encoded by the ZNF684 gene.
C17orf53 is a gene in humans that encodes a protein known as C17orf53, uncharacterized protein C17orf53. It has been shown to target the nucleus, with minor localization in the cytoplasm. Based on current findings C17orf53 is predicted to perform functions of transport, however further research into the protein could provide more specific evidence regarding its function.
bMERB domain containing 1 is a gene expressed in humans which has broad expression across the brain. This gene codes for bMERB1 domain-containing protein 1 isoform 1. It is predicted that this gene is involved in actin cytoskeleton regulation, microtubule regulation and glial cell migration.
The Global Biodata Coalition is an organization promoting biocuration and fostering support of research funders for the sustainability of biological data resources.
References
- ↑ Karsch-Mizrachi, I.; Nakamura, Y.; Cochrane, G.; International Nucleotide Sequence Database Collaboration (2011). "The International Nucleotide Sequence Database Collaboration". Nucleic Acids Research. 40 (Database issue): D33–D37. doi:10.1093/nar/gkr1006. PMC 3244996 . PMID 22080546.
- ↑ Brunak, Soren; Danchin, Antoine; Hattori, Masahira; Nakamura, Haruki; Shinozaki, Kazuo; Matise, Tara; Preuss, Daphne (15 November 2002). "Nucleotide sequence database policies". Science. 298 (5597): 1333. doi:10.1126/science.298.5597.1333b. ISSN 1095-9203. PMID 12436968. S2CID 42740562.
- ↑ "INSDC :: Advisors". Archived from the original on 2007-12-09. Retrieved 2019-06-29.
- ↑ "The DDBJ/ENA/GenBank Feature Table Definition". Ebi.ac.uk. Archived from the original on 2005-03-24. Retrieved 2019-06-29.
- ↑ "European Nucleotide Archive < EMBL-EBI". www.ebi.ac.uk.
- ↑ "Database Browsing". Archived from the original on 2005-02-12. Retrieved 2005-03-02.
- ↑ USA (2019-05-06). "Trifolium repens mRNA for non-cyanogenic beta-glucosidase - Nucleotide - NCBI". Ncbi.nlm.nih.gov. Retrieved 2019-06-29.
