TE-nester: a recursive software tool for structure-based discovery of nested transposable elements

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14330%2F18%3A00107385" target="_blank" >RIV/00216224:14330/18:00107385 - isvavai.cz</a>

Result on the web

<a href="http://dx.doi.org/10.1109/BIBM.2018.8621071" target="_blank" >http://dx.doi.org/10.1109/BIBM.2018.8621071</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1109/BIBM.2018.8621071" target="_blank" >10.1109/BIBM.2018.8621071</a>

Result language

angličtina

Original language name

TE-nester: a recursive software tool for structure-based discovery of nested transposable elements

Original language description

ukaryotic 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. TEnester 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

—

Czech description

—

Type

D - Article in proceedings

CEP classification

—

OECD FORD branch

10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)

Project

<a href="/en/project/GA18-00258S" target="_blank" >GA18-00258S: The role of transposable elements in the dynamics of plant genomes</a><br>

Continuities

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year

2018

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Article name in the collection

Proceedings 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

ISBN

9781538654880

ISSN

2156-1125

e-ISSN

—

Number of pages

3

Pages from-to

2776-2778

Publisher name

IEEE

Place of publication

Neuveden

Event location

Madrid

Event date

Dec 3, 2018

Type of event by nationality

WRD - Celosvětová akce

UT code for WoS article

000458654000484