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.
The Protein Information Resource (PIR), located at Georgetown University Medical Center, is an integrated public bioinformatics resource to support genomic and proteomic research, and scientific studies. It contains protein sequences databases
The Saccharomyces Genome Database (SGD) is a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae, which is commonly known as baker's or budding yeast. Further information is located at the Yeastract curated repository.
MicrobesOnline is a publicly and freely accessible website that hosts multiple comparative genomic tools for comparing microbial species at the genomic, transcriptomic and functional levels. MicrobesOnline was developed by the Virtual Institute for Microbial Stress and Survival, which is based at the Lawrence Berkeley National Laboratory in Berkeley, California. The site was launched in 2005, with regular updates until 2011.
SUPERFAMILY is a database and search platform of structural and functional annotation for all proteins and genomes. It classifies amino acid sequences into known structural domains, especially into SCOP superfamilies. Domains are functional, structural, and evolutionary units that form proteins. Domains of common Ancestry are grouped into superfamilies. The domains and domain superfamilies are defined and described in SCOP. Superfamilies are groups of proteins which have structural evidence to support a common evolutionary ancestor but may not have detectable sequence homology.
Protein function prediction methods are techniques that bioinformatics researchers use to assign biological or biochemical roles to proteins. These proteins are usually ones that are poorly studied or predicted based on genomic sequence data. These predictions are often driven by data-intensive computational procedures. Information may come from nucleic acid sequence homology, gene expression profiles, protein domain structures, text mining of publications, phylogenetic profiles, phenotypic profiles, and protein-protein interaction. Protein function is a broad term: the roles of proteins range from catalysis of biochemical reactions to transport to signal transduction, and a single protein may play a role in multiple processes or cellular pathways.
In molecular biology and genetics, DNA annotation or genome annotation is the process of describing the structure and function of the components of a genome, by analyzing and interpreting them in order to extract their biological significance and understand the biological processes in which they participate. Among other things, it identifies the locations of genes and all the coding regions in a genome and determines what those genes do.
αr7 is a family of bacterial small non-coding RNAs with representatives in a broad group of Alphaproteobacterial species from the order Hyphomicrobiales. The first member of this family was found in a Sinorhizobium meliloti 1021 locus located in the chromosome (C). Further homology and structure conservation analysis identified full-length homologs in several nitrogen-fixing symbiotic rhizobia, in the plant pathogens belonging to Agrobacterium species as well as in a broad spectrum of Brucella species. αr7 RNA species are 134-159 nucleotides (nt) long and share a well defined common secondary structure. αr7 transcripts can be catalogued as trans-acting sRNAs expressed from well-defined promoter regions of independent transcription units within intergenic regions (IGRs) of the Alphaproteobacterial genomes.
αr9 is a family of bacterial small non-coding RNAs with representatives in a broad group of α-proteobacteria from the order Hyphomicrobiales. The first member of this family (Smr9C) was found in a Sinorhizobium meliloti 1021 locus located in the chromosome (C). Further homology and structure conservation analysis have identified full-length Smr9C homologs in several nitrogen-fixing symbiotic rhizobia, in the plant pathogens belonging to Agrobacterium species as well as in a broad spectrum of Brucella species. αr9C RNA species are 144-158 nt long and share a well defined common secondary structure consisting of seven conserved regions. Most of the αr9 transcripts can be catalogued as trans-acting sRNAs expressed from well-defined promoter regions of independent transcription units within intergenic regions (IGRs) of the α-proteobacterial genomes.
αr14 is a family of bacterial small non-coding RNAs with representatives in a broad group of α-proteobacteria. The first member of this family (Smr14C2) was found in a Sinorhizobium meliloti 1021 locus located in the chromosome (C). It was later renamed NfeR1 and shown to be highly expressed in salt stress and during the symbiotic interaction on legume roots. Further homology and structure conservation analysis identified 2 other chromosomal copies and 3 plasmidic ones. Moreover, full-length Smr14C homologs have been identified in several nitrogen-fixing symbiotic rhizobia, in the plant pathogens belonging to Agrobacterium species as well as in a broad spectrum of Brucella species. αr14C RNA species are 115-125 nt long and share a well defined common secondary structure. Most of the αr14 transcripts can be catalogued as trans-acting sRNAs expressed from well-defined promoter regions of independent transcription units within intergenic regions (IGRs) of the α-proteobacterial genomes.
αr35 is a family of bacterial small non-coding RNAs with representatives in a reduced group of Alphaproteobacteria from the order Hyphomicrobiales. The first member of this family (Smr35B) was found in a Sinorhizobium meliloti 1021 locus located in the symbiotic plasmid B (pSymB). Further homology and structure conservation analysis have identified full-length SmrB35 homologs in other legume symbionts, as well as in the human and plant pathogens Brucella anthropi and Agrobacterium tumefaciens, respectively. αr35 RNA species are 139-142 nt long and share a common secondary structure consisting of two stem loops and a well conserved rho independent terminator. Most of the αr35 transcripts can be catalogued as trans-acting sRNAs expressed from well-defined promoter regions of independent transcription units within intergenic regions of the Alphaproteobacterial genomes.
αr45 is a family of bacterial small non-coding RNAs with representatives in a broad group of α-proteobacteria from the order Hyphomicrobiales. The first member of this family (Smr45C) was found in a Sinorhizobium meliloti 1021 locus located in the chromosome (C). Further homology and structure conservation analysis identified homologs in several nitrogen-fixing symbiotic rhizobia, in the plant pathogens belonging to Agrobacterium species as well as in a broad spectrum of Brucella species, in Bartonella species, in several members of the Xanthobactereacea family, and in some representatives of the Beijerinckiaceae family. αr45C RNA species are 147-153 nt long and share a well defined common secondary structure. All of the αr45 transcripts can be catalogued as trans-acting sRNAs expressed from well-defined promoter regions of independent transcription units within intergenic regions (IGRs) of the α-proteobacterial genomes.
In bioinformatics, the PANTHER classification system is a large curated biological database of gene/protein families and their functionally related subfamilies that can be used to classify and identify the function of gene products. PANTHER is part of the Gene Ontology Reference Genome Project designed to classify proteins and their genes for high-throughput analysis.
Gene Ontology (GO) term enrichment is a technique for interpreting sets of genes making use of the Gene Ontology system of classification, in which genes are assigned to a set of predefined bins depending on their functional characteristics. For example, the gene FasR is categorized as being a receptor, involved in apoptosis and located on the plasma membrane.
Gene set enrichment analysis (GSEA) (also called functional enrichment analysis or pathway enrichment analysis) is a method to identify classes of genes or proteins that are over-represented in a large set of genes or proteins, and may have an association with different phenotypes (e.g. different organism growth patterns or diseases). The method uses statistical approaches to identify significantly enriched or depleted groups of genes. Transcriptomics technologies and proteomics results often identify thousands of genes, which are used for the analysis.
Single nucleotide polymorphism annotation is the process of predicting the effect or function of an individual SNP using SNP annotation tools. In SNP annotation the biological information is extracted, collected and displayed in a clear form amenable to query. SNP functional annotation is typically performed based on the available information on nucleic acid and protein sequences.
BioBam is a bioinformatics software company located in Valencia, Spain selling software for the analysis of biological data. Its products are used by public and private research organizations around the world. The firm was founded in 2011 by Dr. Stefan Götz and Dr. Ana Conesa. The managing director of BioBam is Dr. Stefan Götz.
PomBase is a model organism database that provides online access to the fission yeast Schizosaccharomyces pombe genome sequence and annotated features, together with a wide range of manually curated functional gene-specific data. The PomBase website was redeveloped in 2016 to provide users with a more fully integrated, better-performing service.
Model organism databases (MODs) are biological databases, or knowledgebases, dedicated to the provision of in-depth biological data for intensively studied model organisms. MODs allow researchers to easily find background information on large sets of genes, plan experiments efficiently, combine their data with existing knowledge, and construct novel hypotheses. They allow users to analyse results and interpret datasets, and the data they generate are increasingly used to describe less well studied species. Where possible, MODs share common approaches to collect and represent biological information. For example, all MODs use the Gene Ontology (GO) to describe functions, processes and cellular locations of specific gene products. Projects also exist to enable software sharing for curation, visualization and querying between different MODs. Organismal diversity and varying user requirements however mean that MODs are often required to customize capture, display, and provision of data.
