6533b872fe1ef96bd12d4450

RESEARCH PRODUCT

REP2: A Web Server to Detect Common Tandem Repeats in Protein Sequences

Kristina KastanoPablo MierMohamed KamelMiguel A. Andrade-navarro

subject

Repetitive Sequences Amino AcidWeb serverProteomeComputer scienceComputational biologycomputer.software_genreEvolution Molecular03 medical and health sciences0302 clinical medicineTandem repeatStructural BiologySequence comparisonHumansAmino Acid SequenceMolecular BiologyConserved Sequence030304 developmental biologySequence (medicine)Comparative genomicsInternet0303 health sciencesMultiple sequence alignmentBacteriaProteinsTandem Repeat SequencesProteomeUniProtSequence Alignmentcomputer030217 neurology & neurosurgery

description

Ensembles of tandem repeats (TRs) in protein sequences expand rapidly to form domains well suited for interactions with proteins. For this reason, they are relatively frequent. Some TRs have known structures and therefore it is advantageous to predict their presence in a protein sequence. However, since most TRs diverge quickly, their detection by classical sequence comparison algorithms is not very accurate. Previously, we developed a method and a web server that used curated profiles and thresholds for the detection of 11 common TRs. Here we present a new web server (REP2) that allows the analysis of TRs in both individual and aligned sequences. We provide currently precomputed analyses for a selection of 78 UniProt reference proteomes. We illustrate how these data can be used to study the evolution of TRs using comparative genomics. REP2 can be accessed at http://cbdm-01.zdv.uni-mainz.de/~munoz/rep/.

yearjournalcountryeditionlanguage
2020-09-29Journal of Molecular Biology
10.1016/j.jmb.2021.166895http://dx.doi.org/10.1016/j.jmb.2021.166895