Tag: nucleic acid sites, features and motifs

The European Nucleotide Archive (ENA) is a globally comprehensive data resource for nucleotide sequence, spanning raw data, alignments and assemblies, functional and taxonomic annotation and rich contextual data relating to sequenced samples and expe ...

The Nucleic Acids Database contains information about experimentally-determined nucleic acids and complex assemblies. NDB can be used to perform searches based on annotations relating to sequence, structure and function, and to download, analyze, and ...

T-DNA insertions in Arabidopsis and their flanking sequence tags.

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 ...

MINAS contains the exact geometric information on the first and second-shell coordinating ligands of every metal ion present in nucleic acid structures that are deposited in the PDB and NDB. Containing also the sequence information of the binding poc ...

The Pocketome is an encyclopedia of conformational ensembles of druggable binding sites that can be identified experimentally from co-crystal structures in the Protein Data Bank. Each Pocketome entry describes a site on a protein surface that is invo ...

Predicted regulons in prokaryotic genomes

Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system

SAGEmap provides a tool for performing statistical tests designed specifically for differential-type analyses of SAGE (Serial Analysis of Gene Expression) data. The data include SAGE libraries generated by individual labs as well as those generated b ...

NAPP (Nucleic Acids Phylogenetic Profile) enables users to retrieve RNA-rich clusters from any genome in a list of 1000+ sequenced bacterial genomes. RNA-rich clusters can be viewed separately or, alternatively, all tiles from RNA-rich clusters can b ...

POcket Similarity Search Using Multiple-Sketches (PoSSuM) includes all the discovered protein-small molecule binding site pairs with annotations of various types (e.g., UniProt, CATH, SCOP, SCOPe, EC number and Gene ontology). PoSSuM enables rapid ex ...

Database of transcription factor binding sites created from systematic literature curation and genome annotation of DNase I footprints for Drosophila.

Inferred Biomolecular Interaction Server: protein-protein, ligand- and nucleic acid-binding sites

Experimental RNA target motifs bound by splicing proteins in humans.

TassDB (TAndem Splice Site DataBase) stores extensive data about alternative splice events at GYNGYN donors and NAGNAG acceptors. These splice events are of subtle nature since they mostly result in the insertion/deletion of a single amino acid or th ...

The Hormone Receptor Target Binding Loci, HRTBLDb database contains hormone receptor binding regions (binding loci) from in vivo ChIP-based high-throughput experiments as well as in silico, computationally predicted, binding motifs and cis-regulatory ...

Database for binding affinities of protein-nucleic acid complexes and their mutants.

2D convolutional neural network model for identifying families of efflux proteins in transporters.