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Repetitive element detection software tools | Protein structure data analysis

Intragenic duplications of genetic material have important biological roles because of their protein sequence and structural consequences.Source text:(Abraham et al., 2008) Swelfe: a detector of internal repeats in sequences and structures.…
Swelfe
Web

Swelfe

Finds internal repeats at three levels. Swelfe identifies repeats by alignment…

Finds internal repeats at three levels. Swelfe identifies repeats by alignment of DNA sequences, amino acids sequences and three dimensional (3D) structures. Preliminarily, 3D structures are encoded…

ReUPred
Desktop

ReUPred Repeat Protein Unit Predictor

A software tool for the classification and identification of repetitive…

A software tool for the classification and identification of repetitive elements in tandem repeat (TR) proteins. ReUPred concentrates on the solenoid proteins, since it is one of the most abundant…

SymD
Desktop
Web

SymD

A program that detects proteins with internal symmetry. SymD proved to be…

A program that detects proteins with internal symmetry. SymD proved to be useful for analyzing protein structure, function and modeling. This web-based interactive tool was developed by implementing…

TAPO
Web

TAPO TAndem PrOtein detector

A program to identify tandem repeats in protein structures. TAPO uses…

A program to identify tandem repeats in protein structures. TAPO uses periodicities of atomic coordinates and other types of structural representation, including strings generated by conformational…

CE-symm
Desktop
Web

CE-symm

Detects pseudo-symmetry within the tertiary structure of protein chains. Using…

Detects pseudo-symmetry within the tertiary structure of protein chains. Using a large manually curated benchmark of 1007 protein domains, we show that CE-Symm performs significantly better than…

RAPHAEL
Web

RAPHAEL

A method for the accurate determination of solenoid repeats from PDB…

A method for the accurate determination of solenoid repeats from PDB structures. It reliably solves three problems of increasing difficulty: (1) recognition of solenoid domains, (2) determination of…

AnkPred
Web
Desktop

AnkPred Ankyrin Repeat Identification by Graph Spectral Analysis

Provides an elegant and computationally efficient graph-based approach for…

Provides an elegant and computationally efficient graph-based approach for detecting Ankyrin structural repeats in proteins. By analyzing the eigen spectra of the protein structure graph and…

ConSole
Web
Desktop

ConSole

A method to determine the presence and specific positions of individual…

A method to determine the presence and specific positions of individual solenoid repeat units within protein structures. Template matching, a popular image-processing procedure, applied to contact…

ProSTRIP
Web

ProSTRIP

Finds similar structural repeats in a three-dimensional protein structure.…

Finds similar structural repeats in a three-dimensional protein structure. ProSTRIP uses the protein backbone dihedral angles (computed using the four consecutive Cα atoms) for repeat detection.…

OPAAS
Web

OPAAS

A protein structure comparison (PSC) server with the functionality to report…

A protein structure comparison (PSC) server with the functionality to report statistically significant alternative alignments and structural permutations at all levels of complexity. OPAAS deduces…

REPETITA
Web

REPETITA

A method for the detection of solenoid repeats from their amino-acid sequence.…

A method for the detection of solenoid repeats from their amino-acid sequence. REPETITA is based on a metric characterizing amino-acid properties (polarity, secondary structure, molecular volume,…

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