# 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 |
| ard2 | 2013 | web | annotated sequence | Neural network | no | alpha-solenoid |
| DECIPHER | 2021 | downloadable | | Detection of tandem and/or interspersed repeats by orthology (DetectRepeats function in R package) | yes | no |
| TRUST | 2004 | downloadable / web | unit position, multiple sequence alignment | Ab-initio determination of internal repeats in proteins. Exploits transitivity of alignments | ? | no |
| T-REKS | 2009 | downloadable / web | repeat unit | Clustering of lengths between identical short strings by using a K-means algorithm | yes | no |
| 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 | |
| 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 |
| 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 |
| 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 | |
| DOTTER | 1995 | downloadable | | Graphical dotplot program for detailed comparison of two sequences | | |
| 0J.PY | | | | | | |
| PTRStalker | 2012 | downloadable | unit position, multiple sequence alignment | Ab-initio detection of fuzzy tandem repeats in protein amino acid sequences. | | no |
| TRDistiller | 2015 | | | Rapid sorting of tandem repeat (TR)- and no-TR-containing sequences | | |
| 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 |
| REP | 2000 | web | | | no | yes |

## Structure-based annotation methods

| Name | Last update | Usage | Result types | Description | Open source? | Repeat type specific |
| 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 |
| 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 |
| RAPHAEL | 2012 | web | repeat probability | Reduce to three dimensional structure to a wave function. It then determines periodicity information. | no | no |
| 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 | | | | | |