TE-nester: a recursive software tool for structure-based discovery of nested transposable elements
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F68081707%3A_____%2F18%3A00503226" target="_blank" >RIV/68081707:_____/18:00503226 - isvavai.cz</a>
Result on the web
<a href="https://ieeexplore.ieee.org/document/8621071" target="_blank" >https://ieeexplore.ieee.org/document/8621071</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1109/BIBM.2018.8621071" target="_blank" >10.1109/BIBM.2018.8621071</a>
Alternative languages
Result language
angličtina
Original language name
TE-nester: a recursive software tool for structure-based discovery of nested transposable elements
Original language description
Eukaryotic genomes are generally rich in repetitive sequences. LTR retrotransposons are the most abundant class of repetitive sequences in plant genomes. They form segments of genomic sequences that accumulate via individual events and bursts of retrotransposition. A limited number of tools exist that can identify fragments of repetitive sequences that likely originate from a longer, originally unfragmented element, using mostly sequence similarity to guide reconstruction of fragmented sequences. Here, we use a slightly different approach based on structural (as opposed to sequence similarity) detection of unfragmented full-length elements, which are then recursively eliminated from the analyzed sequence to repeatedly uncover unfragmented copies hidden underneath more recent insertions. This approach has the potential to detect relatively old and highly fragmented copies. We created a software tool for this kind of analysis called TE-nester and applied it to a number of assembled plant genomes to discover pairs of nested LTR retrotransposons of various age and fragmentation state. TE-nester will allow us to test hypotheses about genome evolution, TE life cycle and insertion history. The software, still under improvement, is available for download from a repository at https://gitlab.fi.muni.cz/lexa/nested.
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
10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)
Result continuities
Project
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Continuities
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace
Others
Publication year
2018
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Proceedings 2018 IEEE International Conference on Bioinformatics and Biomedecine (BIBM)
ISSN
2156-1125
e-ISSN
—
Volume of the periodical
2018
Issue of the periodical within the volume
2018
Country of publishing house
US - UNITED STATES
Number of pages
3
Pages from-to
2776-2778
UT code for WoS article
000458654000484
EID of the result in the Scopus database
2-s2.0-85062481735