 | This article relies largely or entirely on a single source .(November 2021) |
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| Description | pseudogene annotation. |
| Contact | |
| Primary citation | Karro & al. (2007) [1] |
| Release date | 2006 |
| Access | |
| Website | http://www.pseudogene.org |
Pseudogene is a database of pseudogenes annotations compiled from various sources. [1]
Pseudogenes are nonfunctional segments of DNA that resemble functional genes. Most arise as superfluous copies of functional genes, either directly by DNA duplication or indirectly by reverse transcription of an mRNA transcript. Pseudogenes are usually identified when genome sequence analysis finds gene-like sequences that lack regulatory sequences needed for transcription or translation, or whose coding sequences are obviously defective due to frameshifts or premature stop codons.
An image retrieval system is a computer system used for browsing, searching and retrieving images from a large database of digital images. Most traditional and common methods of image retrieval utilize some method of adding metadata such as captioning, keywords, title or descriptions to the images so that retrieval can be performed over the annotation words. Manual image annotation is time-consuming, laborious and expensive; to address this, there has been a large amount of research done on automatic image annotation. Additionally, the increase in social web applications and the semantic web have inspired the development of several web-based image annotation tools.
In computational biology, gene prediction or gene finding refers to the process of identifying the regions of genomic DNA that encode genes. This includes protein-coding genes as well as RNA genes, but may also include prediction of other functional elements such as regulatory regions. Gene finding is one of the first and most important steps in understanding the genome of a species once it has been sequenced.
Hibernate ORM is an object–relational mapping tool for the Java programming language. It provides a framework for mapping an object-oriented domain model to a relational database. Hibernate handles object–relational impedance mismatch problems by replacing direct, persistent database accesses with high-level object handling functions.
The Gene Ontology (GO) is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species. More specifically, the project aims to: 1) maintain and develop its controlled vocabulary of gene and gene product attributes; 2) annotate genes and gene products, and assimilate and disseminate annotation data; and 3) provide tools for easy access to all aspects of the data provided by the project, and to enable functional interpretation of experimental data using the GO, for example via enrichment analysis. GO is part of a larger classification effort, the Open Biomedical Ontologies, being one of the Initial Candidate Members of the OBO Foundry.
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, United States.
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. Institute leaders such as Rolf Apweiler, Alex Bateman, Ewan Birney, and Guy Cochrane, an adviser on the National Genomics Data Center Scientific Advisory Board, serve as part of the international research network of the BIG Data Center at the Beijing Institute of Genomics.
Pfam is a database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models. The most recent version, Pfam 34.0, was released in March 2021 and contains 19,179 families.
MIRIAM is a community-level effort to standardize the annotation and curation processes of quantitative models of biological systems. It consists of a set of guidelines suitable for use with any structured format, allowing different groups to collaborate and share resulting models. Adherence to these guidelines also facilitates the sharing of software and service infrastructures built upon modeling activities.
Rfam is a database containing information about non-coding RNA (ncRNA) families and other structured RNA elements. It is an annotated, open access database originally developed at the Wellcome Trust Sanger Institute in collaboration with Janelia Farm, and currently hosted at the European Bioinformatics Institute. Rfam is designed to be similar to the Pfam database for annotating protein families.
39S ribosomal protein L20, mitochondrial is a protein that in humans is encoded by the MRPL20 gene.
39S ribosomal protein L1, mitochondrial is a protein that in humans is encoded by the MRPL1 gene.
Putative ATP-binding cassette transporter sub-family C member 13 is a protein that is not present in humans. In humans, ABCC13 is a pseudogene.
The Vertebrate Genome Annotation (VEGA) database is a biological database dedicated to assisting researchers in locating specific areas of the genome and annotating genes or regions of vertebrate genomes. The VEGA browser is based on Ensembl web code and infrastructure and provides a public curation of known vertebrate genes for the scientific community. The VEGA website is updated frequently to maintain the most current information about vertebrate genomes and attempts to present consistently high-quality annotation of all its published vertebrate genomes or genome regions. VEGA was developed by the Wellcome Trust Sanger Institute and is in close association with other annotation databases, such as ZFIN, the Havana Group and GenBank. Manual annotation is currently more accurate at identifying splice variants, pseudogenes, polyadenylation features, non-coding regions and complex gene arrangements than automated methods.
GENCODE is a scientific project in genome research and part of the ENCODE scale-up project.
GeneCards is a database of human genes that provides genomic, proteomic, transcriptomic, genetic and functional information on all known and predicted human genes. It is being developed and maintained by the Crown Human Genome Center at the Weizmann Institute of Science.
DNA annotation or genome annotation is the process of identifying the locations of genes and all of the coding regions in a genome and determining what those genes do. An annotation is a note added by way of explanation or commentary. Once a genome is sequenced, it needs to be annotated to make sense of it. Genes in eukaryotic genome can be annotated using FINDER.
The Consensus Coding Sequence (CCDS) Project is a collaborative effort to maintain a dataset of protein-coding regions that are identically annotated on the human and mouse reference genome assemblies. The CCDS project tracks identical protein annotations on the reference mouse and human genomes with a stable identifier, and ensures that they are consistently represented by the National Center for Biotechnology Information (NCBI), Ensembl, and UCSC Genome Browser. The integrity of the CCDS dataset is maintained through stringent quality assurance testing and on-going manual curation.
Knowledge extraction is the creation of knowledge from structured and unstructured sources. The resulting knowledge needs to be in a machine-readable and machine-interpretable format and must represent knowledge in a manner that facilitates inferencing. Although it is methodically similar to information extraction (NLP) and ETL, the main criterion is that the extraction result goes beyond the creation of structured information or the transformation into a relational schema. It requires either the reuse of existing formal knowledge or the generation of a schema based on the source data.
WormBase is an online biological database about the biology and genome of the nematode model organism Caenorhabditis elegans and contains information about other related nematodes. WormBase is used by the C. elegans research community both as an information resource and as a place to publish and distribute their results. The database is regularly updated with new versions being released every two months. WormBase is one of the organizations participating in the Generic Model Organism Database (GMOD) project.
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