An object database is a database management system in which information is represented in the form of objects as used in object-oriented programming. Object databases are different from relational databases which are table-oriented. Object-relational databases are a hybrid of both approaches.
A ρ factor is a prokaryotic protein involved in the termination of transcription. Rho factor binds to the transcription terminator pause site, an exposed region of single stranded RNA after the open reading frame at C-rich/G-poor sequences that lack obvious secondary structure.
In genetics, a transcription terminator is a section of nucleic acid sequence that marks the end of a gene or operon in genomic DNA during transcription. This sequence mediates transcriptional termination by providing signals in the newly synthesized transcript RNA that trigger processes which release the transcript RNA from the transcriptional complex. These processes include the direct interaction of the mRNA secondary structure with the complex and/or the indirect activities of recruited termination factors. Release of the transcriptional complex frees RNA polymerase and related transcriptional machinery to begin transcription of new mRNAs.
The Entrez Global Query Cross-Database Search System is a federated search engine, or web portal that allows users to search many discrete health sciences databases at the National Center for Biotechnology Information (NCBI) website. The NCBI is a part of the National Library of Medicine (NLM), which is itself a department of the National Institutes of Health (NIH), which in turn is a part of the United States Department of Health and Human Services. The name "Entrez" was chosen to reflect the spirit of welcoming the public to search the content available from the NLM.
In computing, a solution stack or software stack is a set of software subsystems or components needed to create a complete platform such that no additional software is needed to support applications. Applications are said to "run on" or "run on top of" the resulting platform.
In molecular biology and genetics, transcription coregulators are proteins that interact with transcription factors to either activate or repress the transcription of specific genes. Transcription coregulators that activate gene transcription are referred to as coactivators while those that repress are known as corepressors. The mechanism of action of transcription coregulators is to modify chromatin structure and thereby make the associated DNA more or less accessible to transcription. In humans several dozen to several hundred coregulators are known, depending on the level of confidence with which the characterisation of a protein as a coregulator can be made. One class of transcription coregulators modifies chromatin structure through covalent modification of histones. A second ATP dependent class modifies the conformation of chromatin.
Bacterial transcription is the process in which messenger RNA transcripts of genetic material in bacteria are produced, to be translated for the production of proteins. Unlike in eukaryotes, bacterial transcription and translation can occur simultaneously in the cytoplasm. This is impossible in eukaryotes, where transcription occurs in a membrane-bound nucleus while translation occurs outside the nucleus in the cytoplasm. In bacteria genetic material is not enclosed in a membrane-enclosed nucleus and has access to ribosomes in the cytoplasm.
In the field of molecular biology, a corepressor is a substance that inhibits the expression of genes. In prokaryotes, corepressors are small molecules whereas in eukaryotes, corepressors are proteins. A corepressor does not directly bind to DNA, but instead indirectly regulates gene expression by binding to repressors.
The Indexed Database API is a JavaScript application programming interface (API) provided by web browsers for managing a NoSQL database of JSON objects. It is a standard maintained by the World Wide Web Consortium (W3C).
Amazon Relational Database Service is a distributed relational database service by Amazon Web Services (AWS). It is a web service running "in the cloud" designed to simplify the setup, operation, and scaling of a relational database for use in applications. Administration processes like patching the database software, backing up databases and enabling point-in-time recovery are managed automatically. Scaling storage and compute resources can be performed by a single API call as AWS does not offer an ssh connection to RDS instances.
ASPicDB is a database of human protein variants generated by alternative splicing, a process by which the exons of the RNA produced by transcription of a gene are reconnected in multiple ways during RNA splicing.
The Mammalian Promoter Database (MPromDb) is a curated database of gene promoters identified from ChIP-seq The proximal promoter region contains the cis-regulatory elements of most of the transcription factors (TFs).
RegulonDB is a database of the regulatory network of gene expression in Escherichia coli K-12. RegulonDB also models the organization of the genes in transcription units, operons and regulons. A total of 120 sRNAs with 231 total interactions which all together regulate 192 genes are also included. RegulonDB was founded in 1998 and also contributes data to the EcoCyc database.
The Dragon Database for Human Transcription Co-Factors and Transcription Factor Interacting Proteins (TcoF-DB) is a database that facilitates the exploration of proteins involved in the regulation of transcription in humans by binding to regulatory DNA regions and proteins involved in the regulation of transcription in humans by interacting with transcription factors and not binding to regulatory DNA regions. The database describes a total of 529 (potential) human transcription co-factors interacting with a total of 1365 human transcription factors.
Amazon DynamoDB is a fully managed proprietary NoSQL database service that supports key-value and document data structures and is offered by Amazon.com as part of the Amazon Web Services portfolio. DynamoDB exposes a similar data model to and derives its name from Dynamo, but has a different underlying implementation. Dynamo had a multi-master design requiring the client to resolve version conflicts and DynamoDB uses synchronous replication across multiple datacenters for high durability and availability. DynamoDB was announced by Amazon CTO Werner Vogels on January 18, 2012 and is presented as an evolution of Amazon SimpleDB solution.
MIPModDB is a database of comparative protein structure models of MIP family of proteins.
GeNMR method is the first fully automated template-based method of protein structure determination that utilizes both NMR chemical shifts and NOE -based distance restraints.
In molecular biology, MobiDB is a curated biological database designed to offer a centralized resource for annotations of intrinsic protein disorder. Protein disorder is a structural feature characterizing a large number of proteins with prominent members known as intrinsically unstructured proteins. The database features three levels of annotation: manually curated, indirect and predicted. By combining different data sources of protein disorder into a consensus annotation, MobiDB aims at giving the best possible picture of the "disorder landscape" of a given protein of interest.
JASPAR is an open access and widely used database of manually curated, non-redundant transcription factor (TF) binding profiles stored as position frequency matrices (PFM) and transcription factor flexible models (TFFM) for TFs from species in six taxonomic groups. From the supplied PFMs, users may generate position-specific weight matrices (PWM). The JASPAR database was introduced in 2004. There were five major updates and new releases in 2006, 2008, 2010, 2014, 2016 and 2018, which is the latest release of JASPAR.
