PLOTREP: a web tool for defragmentation and visual analysis of dispersed genomic repeats

Identification of dispersed or interspersed repeats, most of which are derived from transposons, retrotransposons or retrovirus-like elements, is an important step in genome annotation. Software tools that compare genomic sequences with precompiled repeat reference libraries using sensitive similarity-based methods provide reliable means of finding the positions of fragments homologous to known repeats. However, their output is often incomplete and fragmented owing to the mutations (nucleotide substitutions, deletions or insertions) that can result in considerable divergence from the reference sequence. Merging these fragments to identify the whole region that represents an ancient copy of a mobile element is challenging, particularly if the element is large and suffered multiple deletions or insertions. Here we report PLOTREP, a tool designed to post-process results obtained by sequence similarity search and merge fragments belonging to the same copy of a repeat. The software allows rapid visual inspection of the results using a dot-plot like graphical output. The web implementation of PLOTREP is available at

DoOP: Databases of Orthologous Promoters, collections of clusters of orthologous upstream sequences from chordates and plants

DoOP (http://doop.abc.hu/) is a database of eukaryotic promoter sequences (upstream regions) aiming to facilitate the recognition of regulatory sites conserved between species. The annotated first exons of human and Arabidopsis thaliana genes were used as queries in BLAST searches to collect the most closely related orthologous first exon sequences from Chordata and Viridiplantae species. Up to 3000 bp DNA segments upstream from these first exons constitute the clusters in the chordate and plant sections of the Database of Orthologous Promoters. Release 1.0 of DoOP contains 21 061 chordate clusters from 284 different species and 7548 plant clusters from 269 different species. The database can be used to find and retrieve promoter sequences of a given gene from various species and it is also suitable to see the most trivial conserved sequence blocks in the orthologous upstream regions. Users can search DoOP with either sequence or text (annotation) to find promoter clusters of various genes. In addition to the sequence data, the positions of the conserved sequence blocks derived from multiple alignments, the positions of repetitive elements and the positions of transcription start sites known from the Eukaryotic Promoter Database (EPD) can be viewed graphically

TECTOP-Magyarország. Jelenkori deformáció és tektonikus topográfia Magyarország területén: aktív szerkezetek, szeizmotektonikus viszonyok, vízhálózat fejlődés és medenceinverzió dinamikája = TECTOP-Hungary. Ongoing deformation pattern and tectonic topography in Hungary: Active structures, seismotectonic habitat, river network development and dynamics of basin inversion

A projekt keretében Magyarország fiatal deformációját és felszínfejlődését vizsgáltuk. Általános érvényű megfigyelésünk szerint hazánkban jelenleg is aktív tektonikai folyamatok zajlanak, amelyek megértése és kvantitatív jellemzése nem csak tudományos feladat, hanem a társadalmi kihatásokat tekintve is kiemelkedő fontosságú. Geofizikai adatrendszerek együttes szerkezeti elemzése kimutatta, hogy a térség jelenkori deformációja alapvetően egykori törésvonalak ismételt felújulásához kötődik. A szerkezetek bonyolult geometriával rendelkező nyírási övekbe rendeződnek, jellemzően KÉK-NyDNy-i csapással. Az aljzat szerkezeti felépítéséhez igazodó fiatal szerkezetek ismételt (szeizmo)tektonikus felújulása ismerhető fel. Geokronológiai vizsgálati eredményeink segítségével előrelépést tettünk a negyedidőszaki vertikális kéregmozgás és felszínfejlődés rekonstruálásában. A Dunántúlra meghatározott kiemelkedési és lepusztulási ráták 0,1-2 mm/év értékek között változnak. Hasonló sebességűek az űrgeodéziai adatok alapján becsült horizontális kéregmozgások is. Aktív tektonika és hidrográfia kapcsolatának vizsgálata alapján kiderült, hogy a jelenkori differenciált függőleges kéregmozgások alapvetően befolyásolják a vízfolyások geometriai viszonyait. A medenceinverzió analóg modellezési eredményei azt mutatják, hogy a Pannon-medence elsőrendű geomorfológiai habitusa kielégítően magyarázható a litoszféra nagyléptékű gyűrődésével. | The project aimed at the investigation of neotectonic deformation and surface evolution in Hungary. In general, it is recognised that the study area is characterised by active tectonic processes. The understanding and quantification of these processes represent a major scientific challenge and is of key importance considering their societal impact. The joint analysis of various geophysical datasets indicates that present-day deformation is mainly related to the reactivation of pre-existing faults. These faults are aligned in ENE-WSW oriented shear zones with rather complex internal geometry. These fracture systems are prone to repeated reactivation in the future, as also manifested in the morphotectonic habitat of the region. Geochronological studies assist the reconstruction of the Quaternary vertical deformation pattern and the main features of landscape development. Uplift and denudation rates for Transdanubia range between 0.1-2 mm/yr, whereas GPS measurements resulted in similar values for the rate of horizontal deformations. An intimate link between active tectonics and hydrography has been established suggesting that differential vertical surface movements have a major role in influencing the spatial arrangement and geometry of rivers. The results of analogue modelling show that the principle geomorphological character of the Pannonian basin can be adequately explained by large-scale folding of the lithosphere and related vertical deformation

Retrospective Detection and Complete Genomic Sequencing of Canine morbillivirus in Eurasian Otter (Lutra lutra) Using Nanopore Technology

The Eurasian otter (Lutra lutra) is a piscivorous apex predator in aquatic habitats, and a flagship species of conservation biology throughout Europe. Despite the wide distribution and ecological relevance of the species, there is a considerable lack of knowledge regarding its virological and veterinary health context, especially in Central Europe. Canine morbillivirus (Canine distemper virus (CDV)) is a highly contagious viral agent of the family Paramyxoviridae with high epizootic potential and veterinary health impact. CDV is present worldwide among a wide range of animals; wild carnivores are at particular risk. As part of a retrospective study, lung-tissue samples (n = 339) from Eurasian otters were collected between 2000 and 2021 throughout Hungary. The samples were screened for CDV using a real-time RT-PCR method. Two specimens proved positive for CDV RNA. In one sample, the complete viral genome was sequenced using a novel, pan-genotype CDV-specific amplicon-based sequencing method with Oxford Nanopore sequencing technology. Both viral sequences were grouped to a European lineage based on the hemagglutinin-gene phylogenetic classification. In this article, we present the feasibility of road-killed animal samples for understanding the long-term dynamics of CDV among wildlife and provide novel virological sequence data to better understand CDV circulation and evolution