List of protein tandem repeat annotation software
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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 |