Comparative analysis of repeat content in plant genomes, large and small.
Name
fpls-14-1103035.pdf
Description
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Size
2.4 MB
Format
Adobe PDF
Checksum (CRC64NVME)
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Resource type
Journal article
Date published
July 14, 2023
Abstract
The DNA Features pipeline is the analysis pipeline at EMBL-EBI that annotates repeat elements, including transposable elements. With Ensembl’s goal to stay at the cutting edge of genome annotation, we proved that this pipeline needed an update. We then created a new analysis that allowed the Ensembl database to store the repeat classification from the PGSB repeat classification (Recat). This new dataset was then fetched using Perl scripts and used to prove that the pipeline modification induced a gain in sensitivity. Finally, we performed a comparative analysis of transposable element distribution in all plant species available, raising new questions about transposable elements in certain branches of the taxonomic tree.
Journal title
Frontiers in Plant Science
Volume
14
Article number
1103035
Publisher
Frontiers Media SA
Place of publication
Lausanne, Switzerland
eISSN
1664-462X
Date accepted
June 14, 2023
Official URL
Rights statement
In Copyright
Additional information
IF = 6.627 (22-23)