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Amino acid repeat prediction software tools | Protein sequence analysis

An estimated 25% of all eukaryotic proteins contain repeats, which underlines the importance of duplication for evolving new protein functions. Internal repeats often correspond to structural or functional units in proteins. Methods capable of…
RADAR
Desktop
Web

RADAR Rapid Automatic Detection and Alignment of Repeats in protein sequences

A tool to identify short composition biased and gapped approximate repeats, as…

A tool to identify short composition biased and gapped approximate repeats, as well as complex repeat architectures involving many different types of repeats in a query sequence. RADAR is useful…

T-REKS
Desktop
Web

T-REKS

A program for ab initio identification of the tandem repeats. T-REKS is based…

A program for ab initio identification of the tandem repeats. T-REKS is based on clustering of lengths between identical short strings by using a K-means algorithm. T-REKS being linked to the Protein…

REPRO
Web

REPRO

The program is able to recognize distant repeats in a single query sequence.…

The program is able to recognize distant repeats in a single query sequence. The technique relies on a variation of the Smith-Waterman local alignment strategy to find non-overlapping top-scoring…

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…

Tally
Web

Tally

A scoring tool based on a machine learning approach. Tally is able to achieve a…

A scoring tool based on a machine learning approach. Tally is able to achieve a better separation between sequences with structural tandem repeats (TRs) and sequences of aperiodic structures, than…

HHrep
Web

HHrep

A web server for the de novo identification of repeats in protein sequences,…

A web server for the de novo identification of repeats in protein sequences, which is based on the pairwise comparison of profile hidden Markov models (HMMs). Its main strength is its sensitivity,…

HHrepID
Desktop
Web

HHrepID

A method for the de novo identification of repeats in protein sequences. It is…

A method for the de novo identification of repeats in protein sequences. It is able to detect the sequence signature of structural repeats in many proteins that have not yet been known to possess…

COACH
Desktop

COACH Comparison of Alignments by Constructing Hidden Markov Models

An approach to profile-profile alignment. COACH aligns two multiple sequence…

An approach to profile-profile alignment. COACH aligns two multiple sequence alignments by constructing a profile HMM from one alignment and aligning the other to that HMM. COACH is competitive in…

LSTM
Desktop

LSTM Long Short-Term Memory

A fast model-based recurrent neural network for protein homology detection.…

A fast model-based recurrent neural network for protein homology detection. LSTM automatically extracts indicative patterns for the positive class, but in contrast to profile methods it also extracts…

TRUST
Desktop
Web

TRUST

A method for ab-initio determination of internal repeats in proteins. The high…

A method for ab-initio determination of internal repeats in proteins. The high sensitivity and accuracy of the method is achieved by exploiting the concept of transitivity of alignments. TRUST is a…

TRDistiller
Desktop

TRDistiller

Allows a rapid sorting of tandem repeat (TR)- and no-TR-containing sequences.…

Allows a rapid sorting of tandem repeat (TR)- and no-TR-containing sequences. Furthermore, in contrast to other rapid programs our program efficiently recognized the same type of repeats that the…

ARD
Web

ARD Alpha-Rod Detector

A neural network for the prediction of alpha-rod repeats. Analysis of the…

A neural network for the prediction of alpha-rod repeats. Analysis of the results suggests that ARD discovers more repeat-containing proteins and repeats per protein than sequence similarity based…

REP
Web

REP

An iterative algorithm based on optimal and sub-optimal score distributions…

An iterative algorithm based on optimal and sub-optimal score distributions from profile analysis that estimates the significance of all repeats that are detected in a single sequence. This procedure…

XSTREAM
Desktop
Web

XSTREAM

A powerful genome data-mining tool designed to efficiently identify tandem…

A powerful genome data-mining tool designed to efficiently identify tandem repeat (TR) patterns in biological sequence data. XSTREAM uses a seed-extension strategy coupled with several…

TPRpred
Desktop
Web

TPRpred

A profile-based method which uses a P-value-dependent score offset to include…

A profile-based method which uses a P-value-dependent score offset to include divergent repeat units and which exploits the tendency of repeats to occur in tandem. TPRpred detects not only tetratrico…

Reptile
Desktop
Web

Reptile

A program for proteome-wide probabilistic description of perfect repeats in…

A program for proteome-wide probabilistic description of perfect repeats in proteins. Reptile combined with programs for the prediction of transmembrane domains and GPI-anchoring resulted in an…

LocRepeat
Desktop

LocRepeat

Finds regions of pseudo-periodic repeats in a long sequence. LocRepeat takes a…

Finds regions of pseudo-periodic repeats in a long sequence. LocRepeat takes a DNA, RNA or protein sequence as its input and outputs a region of pseudo-periodic repeats. It also finds the…

FAIR
Web

FAIR Find All Internal Repeats

A web server which has been deployed to identify the internal sequence repeats…

A web server which has been deployed to identify the internal sequence repeats in protein as well as DNA sequences. FAIR has been tested with a protein sequence of more than 35000 residues available…

REPPER
Web

REPPER REPeats and their PERiodicities

Detects and analyzes regions with short gapless repeats in protein sequences or…

Detects and analyzes regions with short gapless repeats in protein sequences or alignments. REPPER is a web server that implements programs using a sliding window, so as to show the boundaries of…

SIMPLE
Web

SIMPLE

An algorithm for the identification of simple sequences in proteins, RNA or…

An algorithm for the identification of simple sequences in proteins, RNA or DNA. SIMPLE provides a general relative simplicity factor for the sequence, representing the amount of repeats of short…

Internal…
Web

Internal Repeats Finder

A fast algorithm to search for repeating fragments within protein sequences.…

A fast algorithm to search for repeating fragments within protein sequences. The technique is based on an extension of the Smith-Waterman algorithm that allows the calculation of sub-optimal…

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