List of protein tandem repeat annotation software

Computational methods use different properties of protein sequences and structures to find, characterize and annotate protein tandem repeats.

Sequence-based annotation methods

Name	Last update	Usage	Result types	Description	Open source?	Repeat type specific	Reference	-
	2013	web	annotated sequence	Neural network	no	alpha-solenoid		-
	2021	downloadable		Detection of tandem and/or interspersed repeats by orthology	yes	no		-
	2004	downloadable / web	unit position, multiple sequence alignment	Ab-initio determination of internal repeats in proteins. Exploits transitivity of alignments	?	no		-
	2009	downloadable / web	repeat unit	Clustering of lengths between identical short strings by using a K-means algorithm	yes	no		-
	2008	downloadable / web		Identification of repeats in protein sequences via HMM-HMM comparison to exploit evolutionary information in the form of multiple sequence alignments of homologs	no			-
	2018	downloadable / web	unit position, multiple sequence alignment	RADAR identifies short composition biased and gapped approximate repeats, as well as complex repeat architectures involving many different types of repeats in a query sequence	yes	no		-
	2007	web	unit position, different periods, multiple sequence alignment	data-mining tool designed to efficiently identify Tandem Repeat patterns in biological sequence data. The program uses a seed-extension strategy coupled with several post-processing algorithms to analyze FASTA-formatted protein or nucleotide sequences	no	no		-
	2007	downloadable		definition for tandem repeats over the edit distance and an efficient, deterministic algorithm for finding these repeats	no	no		-
	2015	downloadable		Detects tandem repeats with both de novo software and sequence profile HMMs; statistical significance analysis of putative tandem repeats, and filtering of redundant predictions	yes			-
	1995	downloadable		Graphical dotplot program for detailed comparison of two sequences				-
0J.PY								-
	2012	downloadable	unit position, multiple sequence alignment	Ab-initio detection of fuzzy tandem repeats in protein amino acid sequences.		no		-
	2015			Rapid sorting of tandem repeat - and no-TR-containing sequences				-
	2000	web		Repeats detection based on a variation of the Smith-Waterman local alignment strategy followed by a graph-based iterative clustering procedure	no	no
	2000	web			no	yes		-

Structure-based annotation methods

Name	Last update	Usage	Result types	Description	Open source?	Repeat type specific	Reference
	2016	web	unit position	Uses periodicities of atomic coordinates and other types of structural representation, including strings generated by conformational alphabets, residue contact maps, and arrangements of vectors of secondary structure elements	no	no
	2014	galaxy	repeat geometry	Detects internally symmetric protein structures through an "alignment scan" procedure in which a protein structure is aligned to itself after circularly permuting the second copy by all possible number of residues	no	no
	2012	web	repeat probability	Reduce to three dimensional structure to a wave function. It then determines periodicity information.	no	no
	2021
	2010
	2004
RQA	2009
	2006
	2009
	2016
	2015
	2017
	2014
	2008
	2021