List of protein tandem repeat annotation software explained

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
ard2	2013	web	annotated sequence	Neural network	no	alpha-solenoid	^[1]
DECIPHER	2021	downloadable		Detection of tandem and/or interspersed repeats by orthology (DetectRepeats function in R package)	yes	no	^[2]
TRUST	2004	downloadable / web	unit position, multiple sequence alignment	Ab-initio determination of internal repeats in proteins. Exploits transitivity of alignments	?	no	^[3]
T-REKS	2009	downloadable / web	repeat unit	Clustering of lengths between identical short strings by using a K-means algorithm	yes	no	^[4]
HHRepID	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		^[5]
RADAR	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	^[6] ^[7]
XSTREAM	2007	web	unit position, different periods, multiple sequence alignment	data-mining tool designed to efficiently identify Tandem Repeat (TR) 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	^[8]
TRED	2007	downloadable		definition for tandem repeats over the edit distance and an efficient, deterministic algorithm for finding these repeats	no	no
TRAL	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		^[9]
DOTTER	1995	downloadable		Graphical dotplot program for detailed comparison of two sequences			^[10]
0J.PY							^[11]
PTRStalker	2012	downloadable	unit position, multiple sequence alignment	Ab-initio detection of fuzzy tandem repeats in protein amino acid sequences.		no	^[12]
TRDistiller	2015			Rapid sorting of tandem repeat (TR)- and no-TR-containing sequences			^[13]
REPRO	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	^[14]
REP	2000	web			no	yes

Structure-based annotation methods

Name	Last update	Usage	Result types	Description	Open source?	Repeat type specific	Reference
TAPO	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	^[15]
SYMD	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	^[16]
RAPHAEL	2012	web	repeat probability	Reduce to three dimensional structure to a wave function. It then determines periodicity information.	no	no	^[17]
CE-SYMM	2021
ProSTRIP	2010
DAVROS	2004
RQA	2009
OPAAS	2006
Gplus	2009
REUPRED	2016
ConSole	2015
RepeatsDB-Lite	2017
PRIGSA	2014
Swelfe	2008
Frustratometer	2021

Notes and References

1. Fournier D, Palidwor GA, Shcherbinin S, Szengel A, Schaefer MH, Perez-Iratxeta C, Andrade-Navarro MA . Functional and genomic analyses of alpha-solenoid proteins . PLOS ONE . 8 . 11 . e79894 . 21 November 2013 . 24278209 . 3837014 . 10.1371/journal.pone.0079894. 2013PLoSO...879894F . free .
2. Wright ES . Using DECIPHER v2.0 to Analyze Big Biological Sequence Data in R . The R Journal . 2015 . 8 . 1 . 352–359 . 26445311 . 4595117 . 10.1186/s12859-015-0749-z . free .
3. Szklarczyk. Radek. Heringa. Jaap. 2004-08-04. Tracking repeats using significance and transitivity. Bioinformatics. 20. Suppl 1 . i311–317. 10.1093/bioinformatics/bth911. 1367-4811. 15262814. free.
4. Jorda. Julien. Kajava. Andrey V.. 2009-10-15. T-REKS: identification of Tandem REpeats in sequences with a K-meanS based algorithm. Bioinformatics. 25. 20. 2632–2638. 10.1093/bioinformatics/btp482. 1367-4811. 19671691. free.
5. Zimmermann. Lukas. Stephens. Andrew. Nam. Seung-Zin. Rau. David. Kübler. Jonas. Lozajic. Marko. Gabler. Felix. Söding. Johannes. Lupas. Andrei N.. 2018-07-20. A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core. Journal of Molecular Biology. Computation Resources for Molecular Biology. 430. 15. 2237–2243. 10.1016/j.jmb.2017.12.007. 29258817. 22415932 . 0022-2836.
6. Heger. Andreas. Holm. Liisa. 2000. Rapid automatic detection and alignment of repeats in protein sequences. Proteins: Structure, Function, and Genetics. 41. 2. 224–237. 10.1002/1097-0134(20001101)41:2<224::aid-prot70>3.0.co;2-z. 10966575. 21757391 . 0887-3585.
7. Lopez. Rodrigo. Paern. Juri. Squizzato. Silvano. Valentin. Franck. Li. Weizhong. McWilliam. Hamish. Goujon. Mickael. 2010-07-01. A new bioinformatics analysis tools framework at EMBL–EBI. Nucleic Acids Research. 38. suppl_2. W695–W699. 10.1093/nar/gkq313. 20439314. 2896090. 0305-1048.
8. Newman. Aaron M.. Cooper. James B.. 2007-10-11. XSTREAM: A practical algorithm for identification and architecture modeling of tandem repeats in protein sequences. BMC Bioinformatics. 8. 1. 382. 10.1186/1471-2105-8-382. 1471-2105. 2233649. 17931424 . free .
9. Anisimova. Maria. Xenarios. Ioannis. Zoller. Stefan. Stockinger. Heinz. Murri. Riccardo. Messina. Antonio. Pečerska. Jūlija. Korsunsky. Alexander. Schaper. Elke. 2015-09-15. TRAL: tandem repeat annotation library. Bioinformatics. 31. 18. 3051–3053. 10.1093/bioinformatics/btv306. 25987568. 1367-4803. free. 20.500.11850/103876. free.
10. Sonnhammer. E. L.. Durbin. R.. 1995-12-29. A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis. Gene. 167. 1–2. GC1–10. 0378-1119. 8566757. 10.1016/0378-1119(95)00714-8.
11. Wise. M. J.. 2001. 0j.py: a software tool for low complexity proteins and protein domains. Bioinformatics. 17. Suppl 1 . S288–295. 1367-4803. 11473020. 10.1093/bioinformatics/17.suppl_1.s288. free.
12. Pellegrini. Marco. Renda. Maria Elena. Vecchio. Alessio. 2012-03-21. Ab initio detection of fuzzy amino acid tandem repeats in protein sequences. BMC Bioinformatics. 13. 3. S8. 10.1186/1471-2105-13-S3-S8. 1471-2105. 3402919. 22536906 . free .
13. Richard. François D.. Kajava. Andrey V.. 2014-06-01. TRDistiller: A rapid filter for enrichment of sequence datasets with proteins containing tandem repeats. Journal of Structural Biology. 186. 3. 386–391. 10.1016/j.jsb.2014.03.013. 24681324. 1047-8477.
14. George. Richard A.. Heringa. Jaap. October 2000. The REPRO server: finding protein internal sequence repeats through the Web. Trends in Biochemical Sciences. 25. 10. 515–517. 10.1016/s0968-0004(00)01643-1. 11203383. 0968-0004.
15. Do Viet. Phuong. Roche. Daniel B.. Kajava. Andrey V.. 2015-09-14. TAPO: A combined method for the identification of tandem repeats in protein structures. FEBS Letters. 589. 19 Pt A. 2611–2619. 10.1016/j.febslet.2015.08.025. 1873-3468. 26320412. free.
16. Tai. Chin-Hsien. Paul. Rohit. KC. Dukka. Shilling. Jeffery D.. Lee. Byungkook. 2014-07-01. SymD webserver: a platform for detecting internally symmetric protein structures. Nucleic Acids Research. 42. Web Server issue. W296–W300. 10.1093/nar/gku364. 0305-1048. 4086132. 24799435.
17. Walsh. Ian. Sirocco. Francesco G.. Minervini. Giovanni. Di Domenico. Tomás. Ferrari. Carlo. Tosatto. Silvio C. E.. 2012-09-08. RAPHAEL: recognition, periodicity and insertion assignment of solenoid protein structures. Bioinformatics. 28. 24. 3257–3264. 10.1093/bioinformatics/bts550. 22962341. 1460-2059. free.