Tag: sequence composition, complexity and repeats

Genome assemblies and aligned annotations for a wide range of vertebrates and model organisms, along with an integrated tool set for visualizing, comparing, analyzing and sharing both publicly available and user-generated genomic datasets.

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 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 ...

Detects this family of direct repeats found in the DNA of many bacteria and archaea.

The UniPROBE (Universal PBM Resource for Oligonucleotide Binding Evaluation) database hosts data generated by universal protein binding microarray (PBM) technology on the in vitro DNA binding specificities of proteins.

The GenBank, EMBL, and DDBJ nucleic acid sequence data banks have from their inception used tables of sites and features to describe the roles and locations of higher order sequence domains and elements within the genome of an organism. In February, ...

RepeatsDB (http://repeatsdb.bio.unipd.it/) is a database of annotated tandem repeat protein structures. Tandem repeats pose a difficult problem for the analysis of protein structures, as the underlying sequence can be highly degenerate. Several repea ...

PDBselect (http://bioinfo.tg.fh-giessen.de/pdbselect/) is a list of representative protein chains with low mutal sequence identity selected from the protein data bank (PDB) to enable unbiased statistics. The list increased from 155 chains in 1992 to ...

Estimates of DNA-binding specificity for protein-DNA complexes in PDB

Satellog is a database that catalogs all pure 1-16 repeat unit satellite repeats in the human genome along with supplementary data. Satellog analyzes each pure repeat in UniGene clusters for evidence of repeat polymorphism.

Protein structures in bound and unbound states

ProRepeat is an integrated curated repository and analysis platform for in-depth research on the biological characteristics of amino acid tandem repeats. ProRepeat collects repeats from all proteins included in the UniProt knowledgebase, together wit ...

Polyglutamine Repeats in Proteins

Repository for well-characterized elastin sequences to facilitate its study. The database has since expanded to include other non-elastin sequences that share elastic properties.

Polymorphic Simple Sequence Repeats Database

An asynchronous server-based application for the prediction of leucine-rich repeat motifs and an integrative database of NOD-like receptors.

Database and software for mitochondrial imperfect interspersed repeats annotation.

Sequence composition dynamics of genes and genomes.

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.

Gateway to publicly accessible CRISPRs database.

A graphical application for detecting known pathogenic short tandem repeats in sequencing data

Comprehensive analysis of SSRs and database construction using all complete gene-coding sequences in major horticultural and representative plants.

Plant Repeat Database (Plantre) provides re-annotated repeat sequences of plant using a uniform pipeline. The current version of plantrep contains 206.04Gb of 396,041,410 repeats from 459 species that were divided into 15 clades based on their phylog ...