Tag: function analysis

Universal Protein resource. A 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 re ...

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 ...

MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program which implements the Fast Fourier Transform (FFT) to optimise protein alignments based on the physical properties of the amino acids. The prog ...

The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function ...

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 ...

GeneCards is a searchable, integrated, database of human genes that provides concise genomic, transcriptomic, genetic, proteomic, functional and disease related information on all known and predicted human genes.

NONCODE is a database of noncoding RNAs (except tRNAs and rRNAs), including long noncoding (lnc) RNAs. Information contained within the database includes human lncRNA–disease relationships and single nucleotide polymorphism-lncRNA–disease relationshi ...

Ontology-based annotation data can be submitted to the Gene Ontology Consortium and other projects (e.g. the Planteome project) in the Gene Association Format 2.1 (GAF 2.1). The annotation flat file format is comprised of 17 tab-delimited fields. Thi ...

The InParanoid database provides a user interface to orthologs inferred by the InParanoid algorithm. InParanoid release 8 is based on the 66 reference proteomes that the 'Quest for Orthologs' community has agreed on using, plus 207 additional proteom ...

Ontology-based annotation data can be submitted to the Gene Ontology Consortium and other projects (e.g. the Planteome project) in the Gene Association Format 2.2 (GAF 2.2). The annotation flat file format is comprised of 17 tab-delimited fields. Thi ...

The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules.

PLAZA is a platform for comparative, evolutionary, and functional genomics. The platform consists of multiple instances, where each instance contains additional genomes, improved genome annotations, new software tools, etc.

The euHCVdb is mainly oriented towards protein sequence, structure and function analyses and structural biology of Hepatitis C Virus.

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 ...

Genome properties is an annotation system whereby functional attributes can be assigned to a genome, based on the presence of a defined set of protein signatures within that genome. This is a reimplementation at EMBL-EBI of a resource previously host ...

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 ...

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 ...

Database developed for functional prediction and annotation of all potential non-synonymous single-nucleotide variants (nsSNVs) and splice-site variants (ssSNVs) in the human genome. It also facilitates the steps of filtering and prioritizing SNVs fr ...

The Network of Cancer Genes (NCG) contains information on duplicability, evolution, protein-protein and microRNA-gene interaction, function, expression and essentiality of cancer genes from manually curated publications . NCG also provides informatio ...

HymenopteraMine integrates genomic data for bees, ants and the parasitoid jewel wasp. Expression and variation data are provided for A. mellifera.

TCRD is the central resource behind the Illuminating the Druggable Genome Knowledge Management Center (IDG-KMC). TCRD contains information about human targets, with special emphasis on four families of targets that are central to the NIH IDG initiati ...

A resource for exploring the evolution of protein function through relationships in sequence, structure, phylogeny and function.

BacMap is a picture atlas of annotated bacterial genomes. It is an interactive visual database containing hundreds of fully labeled, zoomable, and searchable maps of bacterial genomes.

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.

piRBase stores information on piRNAs and piRNA-associated data to support piRNA functional analysis.

The MAR databases is a collection of manually curated marine microbial contextual and sequence databases, based at the Marine Metagenomics Portal. This was developed as a part of the ELIXIR EXCELERATE project in 2017 and is maintained by The Center f ...

GIANT2 (Genome-wide Integrated Analysis of gene Networks in Tissues) is an interactive web server that enables biomedical researchers to analyze their proteins and pathways of interest and generate hypotheses in the context of genome-scale functional ...

Computational Bridge to Experiments

Ortholog groups and trees for 66 proteomes inferred by Hieranoid 2

Functional divergence between the subfamilies of a protein domain family

The ESFO provides a new paradigm for organizing enzyme sequence, structure, and function information, whereby specific elements of enzyme sequence and structure are mapped to specific conserved aspects of function, thus facilitating the functional an ...

EcoliWiki is a community-based resource for the annotation of all non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements.

A database for systems biology of DNA dynamics during the cell life.

Database of proteins classified by their functional surfaces.

A database-integration approach for protein/genome information retrieval.

A search tool for finding variants from specific chromosome coordinates. It is possible to integrate the results in NGS pipeline.

A statistical method for predicting the effects of mutations.