Dear colleagues,
Registration is open for Transmitting Science Online course “Course:
Introduction to transposable element detection using sequencing data,
June 14th-18th, 2021.
Schedule: Online live sessions from Monday to Friday from 13:00 to
17:00 (GMT+2, Madrid time zone), plus 5 hours of participants working
on their own, with tutored exercises.
Instructors: Dr. Anna-Sophie Fiston-Lavier (Institut des Sciences de
l’Evolution de Montpellier, France) and Dr. Emmanuelle Lerat
(Université Lyon 1, France)
For more information, please check the course webpage:
https://www.transmittingscience.com/courses/genetics-and-genomics/introduction-to-transposable-element-detection-using-sequencing-data/ or write to
[log in to unmask]
Course overview
Transposable elements (TEs) can be major components of eukaryotic
genomes. Such repeated sequences, which can make up very large
proportions like about 50% of mammalian genomes to more than 80% in
the genomes of some plants, can promote various types of mutations,
from gene interruption and expression alteration to large-scale
chromosomal rearrangements. They can also promote the formation of new
genes. Despite their deleterious effects, TEs are currently considered
as major actors in genome evolution due the genetic and epigenetic
diversity they can generate.
Even if they have a fundamental biological role, detection and
analysis of TE sequences are still technologically challenging. The
length and quality of sequenced reads make their detection and
annotation difficult (40% detection error). Moreover, the presence of
TEs in a genome can also lead to important assembly errors due to
rearrangement and the merge of repeats, and to difficulties in the
identification of splicing events and in the estimation of gene
expression in transcriptomic analyses. It is thus important to be able
to identify these sequences in genomic and transcriptomic data.
Since several years, a large number of bioinformatic tools have been
developed allowing a better identification of TEs in genomes. New
tools are released regularly to follow the progress of sequencing
technologies but also to answer particular biological questions
allowing to go from the TE annotation in assembled or unassembled
genomes, to insertion polymorphism detection in natural populations.
The result is a particularly large choice for users leading to
difficulties in the determination of the best tool(s) to use according
to the case.
In this course, we aim at proposing an introduction of selected
bioinformatic tools for the detection and analysis of TEs in genomic
data (RepeatMasker, DnaPipeTE, T-lex).
With best regards
Juanvi
--
Juan Vicente Bertó Mengual
Administration
Transmitting Science
www.transmittingscience.com
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