Tag: gene and protein families

The Human Protein Atlas is program started with the aim to map of all the human proteins in cells, tissues and organs using integration of various omics technologies. It consists of three parts: Tissue Atlas showing the distribution of proteins acros ...

The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). Pfam also generates higher-level groupings of related entries, known as clans. A clan is a collection of Pf ...

InterPro is a resource that provides functional analysis of protein sequences by classifying them into families and predicting the presence of domains and important sites. To classify proteins in this way, InterPro uses predictive models, known as si ...

The Conserved Domain Database (CDD) brings together several collections of multiple sequence alignments representing conserved domains, including NCBI-curated domains, which use 3D-structure information to explicitly to define domain boundaries and p ...

SMART (Simple Modular Architecture Research Tool) is a web resource providing simple identification and extensive annotation of protein domains and the exploration of protein domain architectures. It allows the identification and annotation of geneti ...

The SCOP database is a curated both manually and with the use of automated tools. This freely available resource aims to provide a comprehensive description of the structural and evolutionary relationships between all proteins whose structure is know ...

The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them.

PROSITE is a database of protein families and domains. PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them.

This freely accessible database details a comprehensive IUBMB approved classification system for membrane transport proteins known as the Transporter Classification (TC) system. The TC system is analogous to the Enzyme Commission (EC) system for clas ...

Phytozome, the Plant Comparative Genomics portal of the Department of Energy's Joint Genome Institute, provides JGI users and the broader plant science community a hub for accessing, visualizing and analyzing JGI-sequenced plant genomes, as well as s ...

Protein Ontology (PRO) provides an ontological representation of protein-related entities by explicitly defining them and showing the relationships between them. Each PRO term represents a distinct class of entities (including specific modified forms ...

SUPERFAMILY is a database of structural and functional annotation for all proteins and genomes.

The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). The families in Rfam break down into three broad functional classes: non-coding RNA genes ...

ProDom is a comprehensive set of protein domain families automatically generated from the UniProt Knowledge Database.

MatrixDB stores experimental data established by full-length proteins, matricryptins, glycosaminoglycans, lipids and cations. MatrixDB reports interactions with individual polypeptide chains or with multimers (e.g. collagens, laminins, thrombospondin ...

Database for identification and cataloguing of group II introns. All bacterial introns listed are full-length and appear to be functional, based on intron RNA and IEP characteristics. The database names the full-length introns, and provides informati ...

TIGRFAMs is a collection of manually curated protein families focusing primarily on prokaryotic sequences.It consists of hidden Markov models (HMMs), multiple sequence alignments, Gene Ontology (GO) terminology, Enzyme Commission (EC) numbers, gene s ...

OrthoDB presents a catalog of eukaryotic orthologous protein-coding genes. Orthology refers to the last common ancestor of the species under consideration, and thus OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny ...

PRINTS is a collection of groups of conserved protein motifs, called fingerprints, used to define a protein family. A fingerprint is a group of conserved motifs used to characterize a protein family. Usually, the motifs do not overlap, though they ma ...

H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. By extensive analyses of all human transcripts, we provide curated annotations of human genes and transcripts that include gene structures, alternative splici ...

Bacteria and archaea employ dedicated signal transduction systems that modulate gene expression, second-messenger turnover, quorum sensing, biofilm formation, motility, host-pathogen and beneficial interactions. The updated Microbial Signal Transduct ...

Online GEne Essentiality database

ACLAME is a database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons.

HAMAP is a system, based on manual protein annotation, that identifies and semi-automatically annotates proteins that are part of well-conserved families or subfamilies: the HAMAP families. HAMAP is based on manually created family rules and is appli ...

MoonProt Database is a manually curated, searchable, internet-based resource with information about the over 200 proteins that have been experimentally verified to be moonlighting proteins. Moonlighting proteins comprise a class of multifunctional pr ...

Method to assess the outcome of non-synonymous SNVs using a CONsensus DELeteriousness score that combines various tools.

AceView provides a curated, comprehensive and non-redundant sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These experimental cDNA sequences are first co-align ...

The Bacterial protein tYrosine Kinase database (BYKdb) contains computer-annotated BY-kinase sequences. The database web interface allows static and dynamic queries and provides integrated analysis tools including sequence annotation.

We developed a pipeline to annotate lncRNAs (Long non-coding RNAs) and applied it to 37 plant species and six algae, resulting in the annotation of more than 120 000 lncRNAs. To facilitate the study of lncRNAs for the plant research community, the in ...

This resource is a hierarchical clustering of UniProt protein sequences into hierarchical trees. This resource allows for the study of sub-family and super-family of a protein, using UniRef50 clusters.

A suite of Web-based tools for comparative genomics

This database is compiled from the human genome nucleotide sequences obtained mostly in the Human Genome Projects. The database makes it possible to continuously improve classification and characterization of retroviral families. The HERV database no ...

The ASTRAL compendium provides a set of tools and databases designed to aid investigators in the analysis of protein structure, particularly through the use of sequence comparison. Astral augments SCOP, a manual classification of protein domains acco ...

The Database of Arabidopsis Transcription Factors (DATF) collects all Arabidopsis transcription factors (totally 1922 Loci; 2290 Gene Models) and classifies them into 64 families.The Version 2 of DATF was updated at July 2006. It is based on the Arab ...

This is a database of comparative protein structure models of the MIP (Major Intrinsic Protein) family of proteins. The MIPs have been identified from the completed genome sequence of organisms available at NCBI.

The Plant Transcription Factor Database is an integrative database that provides putatively complete sets of transcription factors (TFs) and other transcriptional regulators (TRs) in plant species whose genomes have been completely sequenced and anno ...

HOGENOM is a phylogenomic database providing families of homologous genes and associated phylogenetic trees (and sequence alignments) for a wide set sequenced organisms.

The PIR SuperFamily concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships.

CleanEx is a database which provides access to public gene expression data via unique approved gene symbols and which represents heterogeneous expression data produced by different technologies in a way that facilitates joint analysis and cross-datas ...

Manually annotated component of UniProtKB (produced by the UniProt consortium). It contains manually-annotated (reviewed) records with information extracted from the literature and curator-evaluated computational analysis.

Peroxibase provides access to peroxidase sequences from all kingdoms of life, and provides a series of bioinformatics tools and facilities suitable for analysing these sequences.

GreenPhylDB comprises 37 full genomes from the major phylum of plant evolution. Clustering of these genomes was performed to define a consistent and extensive set of homeomorphic plant families.

GermOnline is a cross-species database gateway focusing on high-throughput expression data relevant for germline development, the meiotic cell cycle and mitosis in healthy versus malignant cells. The portal provides access to the Saccharomyces Genomi ...

The LegumeIP 2.0 database hosts large-scale genomics and transcriptomics data and provides integrative bioinformatics tools for the study of gene function and evolution in legumes.

HOVERGEN is a database of homologous vertebrate genes that allows one to select sets of homologous genes among vertebrate species, and to visualize multiple alignments and phylogenetic trees.

<<<!!!<<< This repository is no longer available >>>!!!>>>

This database contains data on 105 Arabidopsis transcriptome projects (3262 hybridized samples) in public access out of a total of 172 projects (~6440 hybridized samples).

PeroxiRedoxin classification indEX

Gene regulation in bacteriophages

tRNA Gene DataBase Curated by Experts

Blood Group Antigen Gene Mutation Database

Database of homologous genes from Ensembl organisms and Ensembl families, structured under ACNUC sequence database management system.

Protective antigen database and analysis system

Prokaryotic 2-Component Systems database

Plant protease inhibitors (PIs) can be counted among the defensive proteins that plants display to minimize the adverse effects deriving from the attack of phytophagous insects. They are usually present in seeds and storage tissues, but are also expr ...

Structural proteins of Arthropod cuticle

Detection of functional divergence in human protein families. Cube-DB is a database of pre-evaluated conservation and specialization scores for residues in paralogous proteins belonging to multi-member families of human proteins. Protein family class ...

Biosynthetic gene cluster families

Thioester-active enzymes

Database for cross species expression pattern comparisons

Gene Ontology-based functional similarity values for proteins and protein families

Functional divergence between the subfamilies of a protein domain family

SilkDB is a database of the integrated genome resource for the silkworm, Bombyx mori. This database provides access to not only genomic data including functional annotation of genes, gene products and chromosomal mapping, but also extensive biologica ...

Comparative genomics of Fusarium strains

fPOP (footprinting Pockets Of Proteins) is a database of the protein functional surfaces identified by shape analysis. In this relational database, we collected the spatial patterns of protein binding sites including both holo and apo forms from more ...

Non-redundant databases of patent DNA and protein sequences

The Hyperlink Management System (HMS) automatically updates and maintains hyperlinks among major databases using various data IDs (e.g. HUGO Gene Symbols, IDs from PDB, UniProt). The ID Converter System (ICS) supports the conversion of data IDs using ...

A database of prokaryotic defense systems related genes. Procaryotic Antiviral Defense System. procaryotic database, defense system database, pangenome database. PADS Arsenal A Database of Prokaryotic Defense Systems Related Genes.

Phylogenetic Exploration of Viruses and their Evolutionary Relationships

Repository of protein names and naming rules

Laminins (LM) correspond to a large number of heretotrimeric glycoproteins, playing and a major role in several cell functions, including differentiation, proliferation, adhesion, and migration [1-3]. In addition to binding to other extracellular mat ...

ARGminer is a web platform dedicated to the validation of ARGs by using sequence alignment and evidence from multiple sources.

Collection of gene and protein names, organized by species that can be used to search for a given gene/protein name, retrieve all synonyms for this entity, and query Medline with a set of user-selected terms.

The UniProt archive (UniParc), part of the UniProt databases, is an archival protein sequence collection from all major publicly accessible resources. New and revised protein sequences are added daily into UniParc while not deleting the previous vers ...

Database of proteins classified by their functional surfaces.

CpGDB (Chloroplast Genome Database) is a user friendly, freely available and dynamic relational database which allows search and download of complete chloroplast genome sequences, individual gene sequences and feature records of different plant speci ...

EvolClust predicts groups of genes that are conserved in terms of gene order across different species distinguishing it from the background gene order conservation found between species. We define a cluster as a group of homologous proteins that are ...

a genomic database of rice relatives for rice research | Welcome to RiceRelativesGD, a genomic database of rice relatives for rice research! | The cultivated rice (Oryza sativa) is one of the most important crops in the world

Evolutionary-oriented database of RNA recognition motif sequences.

MSRdb (Mycobacterial Systems Resource) is a mycobacterial systems resource for the research community. The Mycobacterial Systems Resource (MSR) is a comprehensive, integrated biological and bioinformatic resource for the research community. The MSR u ...

an integrated resource for glycosyltransferase sequences and annotations. Glycosyltransferases (GTs), a large class of carbohydrate-active enzymes, adds glycosyl moieties to various substrates to generate multiple bioactive compounds, including natu ...

Database and resource of protein families in Arthropod genomes.

dbPUP is a database of polyphenol utilization proteins (PUPs) that have been experimentally characterized to metabolize polyphenol substrates.

DbStRiPs (Database of structural repeats in proteins) is a structural repeat database which classifies a protein structure into a structural repeat family based on graph based structural repeat identification algorithm, PRIGSA2.

Sequences and motifs of the phycobilin lyase protein family

The Spirochetes Genome Browser

<<<!!!<<< This repository is no longer available>>>!!!>>>. Although the web pages are no longer available, you will still be able to download the final UniGene builds as static content from the FTP site https://ftp.ncbi.nlm.nih.gov/repository/UniGen ...

DSDBASE is a database of disulphide bonds in proteins that provides information on native disulphides and those that are stereochemically possible between pairs of residues for all known protein structural entries. The modelling of disulphides has be ...

Structural and functionnal annotation of plant gene and protein families by a network of experts.

An integrated multi-omics database of barley gene families.

Statistical detection of pathogen-associated protein domains.

SulfAtlas describes the family and sub-families of structurally-related sulfatases. Sub-families are created based on phylogenetic analyses and essentially correspond to different substrate specificities.

Comparative transcriptomics and co-expression database for bacterial pathogens.

A simple access point to view gene family assignments, annotations and phylogenetic data for insect immune-related genes and gene families.

Prokaryotic protein phosphatases.

This is the Schizosaccharomyces japonicus genome database.

A collection of related protein sequences (clusters) consists of proteins derived from the annotations of whole genomes, organelles and plasmids. It currently limited to Archaea, Bacteria, Plants, Fungi, Protozoans, and Viruses.

A curated database for comprehensively profiling methane cycling processes of environmental microbiomes.

A Manually Curated Database of Protein Families Mediating the Life Cycle of Bacterial Mobile Genetic Elements.

A collection of genes and proteins involved in human and yeast cell cycle.

MoonDB is a database containing predicted Extreme Multifunctional (EMF) proteins (i.e. proteins with several unrelated functions), as well as a set of manually curated moonlighting proteins. Moonlighting proteins are a subclass of multifunctional pro ...

CoDNaS Quaternary is a high confidence database of conformational diversity in proteins that present a biologically relevant quaternary structure.

A database designed to help the mycologist community to access to fungal DNA markers data for phylogenetic analyses.

Genomicus-fungi is a genome browser that enables users to navigate in fungi genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.

Genomicus-protists is a genome browser that enables users to navigate in protists genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.

Genomicus-metazoa is a genome browser that enables users to navigate in metazoa genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.

Genomicus-tunicates is a genome browser that enables users to navigate in tunicates genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time. It uses ANISEED (htt ...

The Bacterial Microcompartment Database. MCPdb – The Bacterial Microcompartment Databse. MCPDB A bacterial microcompartment database and structure viewer include Carboxysome Pdu Eut BMC BMV MCP organelle encapsulin protein capsid. MCPdb is an onli ...

Genomicus-Plants is a genome browser that enables users to navigate in plants genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.