Tag: sequence sites, features and motifs

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 ...

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.

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 ...

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 ...

The international glycan structure repository for glycans published in the literature. Any glycan structure, ranging in resolution from monosaccharide composition to fully defined structures can be registered and have an accession number assigned as ...

IMGT/LIGM-DB is the IMGT® comprehensive database of immunoglobulin (IG) and T cell receptor (TR) nucleotide sequences, from human and other vertebrate species, with translation for fully annotated sequences, created in 1989 by LIGM (http://www.imgt.o ...

DEPOD - the human DEPhOsphorylation Database is a manually curated database collecting human active and inactive phosphatases, their experimentally verified protein and non-protein substrates, and dephosphorylation site information, and pathways in w ...

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.

Phosphorylation sites in various species identified by mass spectrometry

The IRESite database presents information about experimentally studied IRES (Internal Ribosome Entry Site) segments. IRES regions are known to attract the eukaryotic ribosomal translation initiation complex and thus promote translation initiation ind ...

The cisRED database holds conserved sequence motifs identified by genome scale motif discovery, similarity, clustering, co-occurrence and coexpression calculations. Sequence inputs include low-coverage genome sequence data and ENCODE data.

The primary goal of VDJdb is to facilitate access to existing information on T-cell receptor antigen specificities, i.e. the ability to recognize certain epitopes in certain MHC contexts. Our mission is to both aggregate the scarce TCR specificity in ...

Gypsy database of mobile genetic elements

Allows correlation of GeneChip array results with array design and annotation information; provides access to array content information, including probe sequences and gene annotations; free registration is required.

ParameciumDB is a new model organism database for Paramecium, built using components of the Generic Model Organism Database (http://www.gmod.org) construction set (Chado relational database schema, Turnkey generic web framework and Gbrowse). The data ...

Experimental RNA target motifs bound by splicing proteins in humans.

Predicted targets of host and viral miRNAs

The Tobacco Markers & Primers Database.

Fast and easy retrieval of r-protein sequences from publicly available complete prokaryotic genome sequences.

ConsRM is a collection and large-scale prediction of the evolutionarily conserved RNA methylation sites, with implications for the functional epitranscriptome.

A database portal containing esources that can be used to infer baseline species conditions.

TUPDB (Target-Unrelated Peptide Data Bank) is a comprehensive database of target-unrelated peptides (TUPs) and TUP motifs. It contains extensive information extracted from research articles and public databases.

Expansin Engineering Database integrates information on sequence, structure and function of expansins.

PopTargs is a database for studying population evolutionary genetics of human microRNA target sites. These are the scripts used to create the MySQL database that is used by PopTargs.essex.ac.uk. The pipeline can be altered to create similar database ...

an online database of unspecific peroxygenases. UPObase: Unspecific Peroxygenase Database : Homepage. Unspecific Peroxygenase Database (UPObase) is a genome mining pipeline based database which consists of all the sequences of fungal unspecific per ...

A CRISPR Interactive database.

A webtool to identify and analyze bacterial microcompartment types in sequence data.

LjaFGD is the Lonicera japonica functional genomics database..

ColabFold databases are MMseqs2 expandable profile databases to generate diverse multiple sequence alignments to predict protein structures.

ImitateDB is a comprehensive database for information about molecular mimicry candidates represented as DMPs and MMPs for each experimentally validated unique host pathogen protein-protein interaction.

A web database for sequence and shape motif analyses and identification.

A database of monosaccharide biosynthesis pathways. Monosaccharide Biosynthesis Pathways Database. Pathways for monosaccharide biosynthesis. Welcome to MonoPathDB, a database of biosynthesis pathways and enzymes for monosaccharides.

GPCR-Sequence-Structure-Feature-Extractor (SSFE). Provides template suggestions and homology models of Class A GPCRs. Identifies key sequence and structural motifs in Class A GPCRs to guide template selection and build homology models.

B-AMP is an Antimicrobial Peptide (AMP) repository for biofilms, consisting of a vast library of 5544 structural AMP models, AMPs annotated to relevant biofilm literature, and protein-peptide interaction models with potential biofilm targets.

Calgary approach to ANnoTating HYDrocarbon degradation genes (CANT-HYD), a database of 37 HMMs of marker genes involved in anaerobic and aerobic degradation pathways of aliphatic and aromatic hydrocarbons.