Volkov, K. V. | bioRxiv Science

bioRxiv2026

FuzzyClusTeR: a web server for analysis of tandem and diffuse DNA repeat clusters with application to telomeric-like repeats

DNA repeats constitute a large fraction of eukaryotic genomes and play important roles in genome stability and evolution. While tandem repeats such as microsatellites have been extensively studied, the genomic organization and potential functions of dispersed or loosely organized repeat patterns remain poorly understood. Here we present FuzzyClusTeR, a web server for the identification, visualization and enrichment analysis of DNA repeat clusters in genomic sequences. Using parameterized metrics, FuzzyClusTeR detects both classical tandem repeats and regions where related motifs occur in proximity without forming perfect tandem arrays, which we term diffuse (or fuzzy) repeat clusters. The server supports analysis of user-defined sequences as well as genome-scale datasets, including the T2T-CHM13 and GRCh38 human genome assemblies, and provides interactive visualization and statistical tools for assessing the genomic distribution of repetitive motifs and corresponding clusters. As a demonstration, we analyzed telomeric-like repeats in the T2T-CHM13v2.0 genome and identified families of diffuse clusters enriched in these motifs. Comparison with simulated sequences suggests that these clusters represent non-random genomic patterns with potential evolutionary and functional significance. FuzzyClusTeR enables systematic exploration of repeat clustering across genomic regions or entire genomes. It is available at https://utils.researchpark.ru/bio/fuzzycluster GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=79 SRC="FIGDIR/small/712643v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@1844091org.highwire.dtl.DTLVardef@1ab0e1dorg.highwire.dtl.DTLVardef@12bc717org.highwire.dtl.DTLVardef@11bbec9_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2019

Accumulation of storage proteins in plant seeds is mediated by amyloid formation

Amyloids are protein aggregates with a highly ordered spatial structure giving them unique physicochemical properties. Different amyloids not only participate in the development of numerous incurable diseases but control vital functions in Archaea, Bacteria and Eukarya. Plants are a poorly studied systematic group in the field of amyloid biology. Amyloid properties have not yet been demonstrated for plant proteins under native conditions in vivo. Here we show that seeds of garden pea Pisum sativum L. contain amyloid-like aggregates of storage proteins, the most abundant one, 7S globulin Vicilin, forms bona fide amyloids in vivo and in vitro. The Vicilin amyloid accumulation increases during seed maturation and wanes at germination. Amyloids of Vicilin resist digestion by gastrointestinal enzymes, persist in canned peas and exhibit toxicity for yeast and mammalian cells. Our finding for the first time reveals involvement of amyloid formation in the accumulation of storage proteins in plant seeds.

biochemistry↗