These are results generated from the complete annotation of the Arabidopsis thaliana genome.
Annotated data
This session contains some of the data generated in the TEs annotation. In the SINE annotation, .fa files and overlay images are obtained.
In the LINE annotation, .fa and .gff3 files are obtained. In the complete annotation, more refined data is obtained for the SINEs and LINEs
elements, as well as data on LTRs, TIRs and Helitrons elements. Masked files, .gff3 files, .sum files and .LAI files are also generated. When
using the tool on the local machine, it is possible to obtain more data than just that presented.
Genomic data (.gff3 .fa)
Report
In this session, we are introduced to the annotation report for transposable elements. Transposable elements are classified into classes, orders,
superfamilies and autonomies. These elements are organized based on the number of base pairs and the percentage they occupy in the genome of the
organism analyzed. The data is stored in .txt files, accompanied by bar charts and bubble charts for visualization.
| TEs Report |
Landscape Graphs
In this section, the repeat landscape graphs offer a visual representation of the relative quantity of each Transposable Element (TE) class,
correlated to the Kimura distance on the x-axis, acting as an indicator of time. In contrast, the y-axis displays the comparative coverage of each repeat class,
adjusted for genome size. Thus, the repeat landscape graph provides a coherent inference of the relative ages of each element identified in a specific genome.
LTR SuperFamily
This section shows the histograms of the LTR ages.
The dashed vertical lines indicate the median, while the horizontal line represents the average (in millions of years - Mya).
LTR Phylogeny
In this section, the phylogeny of the alignments of all the LTR-RT domains is elaborated,
providing a comprehensive visualization of the evolutionary relationships between them.
LTR Phylogenetic tree - Density
In this section, the densities of the elements are displayed, with the outer circle (purple) representing the length occupied by each element in base pairs (bp),
while the inner circle (red) reflects the number of occurrences of each element.
This visual representation provides a comprehensive view of the distribution and frequency of the elements under study.
The data in Report, Landscape Graphs, LTR Superfamily, LTR Phylogeny and LTR Phylogenetic tree - Density is only available
when the annotation is complete.