Computational methods use different properties of protein sequences and structures to find, characterize and annotate protein tandem repeats.
Sequence-based annotation methods
NameLast updateUsageResult typesDescriptionOpen source?Repeat type specificReferenceard22013webannotated sequenceNeural networknoalpha-solenoidDECIPHER2021downloadableDetection of tandem and/or interspersed repeats by orthology (DetectRepeats function in R package)yesnoTRUST2004downloadable / webunit position, multiple sequence alignmentAb-initio determination of internal repeats in proteins. Exploits transitivity of alignments?noT-REKS2009downloadable / webrepeat unitClustering of lengths between identical short strings by using a K-means algorithmyesnoHHRepID2008downloadable / webIdentification of repeats in protein sequences via HMM-HMM comparison to exploit evolutionary information in the form of multiple sequence alignments of homologsnoRADAR2018downloadable / webunit position, multiple sequence alignmentRADAR identifies short composition biased and gapped approximate repeats, as well as complex repeat architectures involving many different types of repeats in a query sequenceyesnoXSTREAM2007webunit position, different periods, multiple sequence alignmentdata-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 sequencesnonoTRED2007downloadabledefinition for tandem repeats over the edit distance and an efficient, deterministic algorithm for finding these repeatsnonoTRAL2015downloadableDetects tandem repeats with both de novo software and sequence profile HMMs; statistical significance analysis of putative tandem repeats, and filtering of redundant predictionsyesDOTTER1995downloadableGraphical dotplot program for detailed comparison of two sequences0J.PYPTRStalker2012downloadableunit position, multiple sequence alignmentAb-initio detection of fuzzy tandem repeats in protein amino acid sequences.noTRDistiller2015Rapid sorting of tandem repeat (TR)- and no-TR-containing sequencesREPRO2000webRepeats detection based on a variation of the Smith-Waterman local alignment strategy followed by a graph-based iterative clustering procedurenonoREP2000webnoyes
Structure-based annotation methods
NameLast updateUsageResult typesDescriptionOpen source?Repeat type specificReferenceTAPO2016webunit positionUses 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 elementsnonoSYMD2014galaxyrepeat geometryDetects 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 residuesnonoRAPHAEL2012webrepeat probabilityReduce to three dimensional structure to a wave function. It then determines periodicity information.nonoCE-SYMM2021ProSTRIP2010DAVROS2004RQA2009OPAAS2006Gplus2009REUPRED2016ConSole2015RepeatsDB-Lite2017PRIGSA2014Swelfe2008Frustratometer2021
References