DANTE and DANTE_LTR: lineage-centric annotation pipelines for long terminal repeat retrotransposons in plant genomes
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60077344%3A_____%2F24%3A00598288" target="_blank" >RIV/60077344:_____/24:00598288 - isvavai.cz</a>
Result on the web
<a href="https://academic.oup.com/nargab/article/6/3/lqae113/7744946?login=true" target="_blank" >https://academic.oup.com/nargab/article/6/3/lqae113/7744946?login=true</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1093/nargab/lqae113" target="_blank" >10.1093/nargab/lqae113</a>
Alternative languages
Result language
angličtina
Original language name
DANTE and DANTE_LTR: lineage-centric annotation pipelines for long terminal repeat retrotransposons in plant genomes
Original language description
Long terminal repeat (LTR) retrotransposons constitute a predominant class of repetitive DNA elements in most plant genomes. With the increasing number of sequenced plant genomes, there is an ongoing demand for computational tools facilitating efficient annotation and classification of LTR retrotransposons in plant genome assemblies. Herein, we introduce DANTE, a computational pipeline for Domain-based ANnotation of Transposable Elements, designed for sensitive detection of these elements via their conserved protein domain sequences. The identified protein domains are subsequently inputted into the DANTE_LTR pipeline to annotate complete element sequences by detecting their structural features, such as LTRs, in adjacent genomic regions. Leveraging domain sequences allows for precise classification of elements into phylogenetic lineages, offering a more granular annotation compared with coarser conventional superfamily-based classification methods. The efficiency and accuracy of this approach were evidenced via annotation of LTR retrotransposons in 93 plant genomes. Results were benchmarked against several established pipelines, showing that DANTE_LTR is capable of identifying significantly more intact LTR retrotransposons. DANTE and DANTE_LTR are provided as user-friendly Galaxy tools accessible via a public server (https://repeatexplorer-elixir.cerit-sc.cz), installable on local Galaxy instances from the Galaxy tool shed or executable from the command line.
Czech name
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Czech description
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Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
10603 - Genetics and heredity (medical genetics to be 3)
Result continuities
Project
<a href="/en/project/LM2023055" target="_blank" >LM2023055: Czech National Infrastructure for Biological Data</a><br>
Continuities
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace
Others
Publication year
2024
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
NAR Genomics and Bioinformatics
ISSN
2631-9268
e-ISSN
2631-9268
Volume of the periodical
6
Issue of the periodical within the volume
3
Country of publishing house
GB - UNITED KINGDOM
Number of pages
10
Pages from-to
lqae113
UT code for WoS article
001300170800003
EID of the result in the Scopus database
2-s2.0-85202916086