AnnoTEP documentation - Annotation Transposable Elements for Plants
Welcome to the AnnoTEP documentation.
The AnnoTEP framework was developed to facilitate the annotation of transposable elements in plant genomes and to provide essential support to the scientific community involved in research centered on these elements.
Table of contents
Intalling your Local Web Server
The AnnoTEP tool can be installed and run locally using containers, providing two distinct
interfaces to cater to different types of users: Container Graphical Interface and Container Bash Interface
System requirements
Minimum requirements for both versions for Genomes up to 1GB
More resources are recommended for larger genomes.
Container Graphical Interface
For this version, your machine must have Internet access.
This version can be installed via Docker, as shown in the download section. It has a graphical interface and functions similar to the web server model, with the difference that it works entirely on the user's machine via localhost.
There is no limit to the size of the genome, and the annotation speed will depend on the capacity of your local machine or server. Here you can enter the number of threads you want to use for the complete annotation. Although it works on the local machine, this model integrates an e-mail system that will notify you when the annotation is finished. Also, avoid shutting down the machine during the process, as this can interrupt data analysis.
About annotation and results, you will find in the subtopic Annotation levels and results.
Container Bash Interface
This version works entirely via the command line and does not require Internet access. Like the version with a graphical interface, it has no genome size limit, and the annotation speed will depend on the capacity of the local machine or server. It can be a little more complex to use than the version with a graphical interface.
Your data is entered using predefined parameters. All you have to do is enter the path of the genome on your machine, the type of annotation, and depending on the type of annotation, you can enter the number of threads you want to use. All these steps are described in the download section.
About annotation and results, you will find in the subtopic Annotation levels and results.
Annotation levels and results
Selecting SINE Annotation: This option exclusively analyzes the SINE elements present in the plant genome, generating data in .fa format and superimposed images of the element. In containerized versions, the result of this annotation is stored in the SINE folder.
Selecting LINE Annotation: This option exclusively analyzes the LINE elements present in the plant genome, generating libraries containing LINE sequences in .fa and .gff3 formats. In containerized versions, the result of this annotation is stored in the LINE folder. This option can generate some false positives, making it necessary to carry out the complete annotation to obtain more accurate data.
Selecting SINE and LINE Annotation (Together): Brings the same data generated by their unit versions.
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Selecting Complete Annotation: This option performs an exhaustive analysis of various types of transposable elements, including SINEs, LINEs, LTR, TIR and Helitrons (based on REXdb
Viridiplantae v3.0 and and GyDB nomenclature as proposed by Orozco-Arias et al., 2019). The SINEs and LINEs data generated here is more refined than in the individual versions. In addition, the
result generated by this annotation provides data on the TRIM, LARD, TR_GAG, BARE-2, MITES elements, as well as the Gypsy and Copia families and respective evolutionary lineages. The analysis
also generates graphs and phylogenetic trees of the RT-LTRs, offering a comprehensive and detailed view of the transposable elements present in the genome studied. In addition, this annotation
step masks the genome, helping to identify and suppress repetitive regions, which facilitates subsequent analysis and annotation of the genome.
For more information, visit the tool's repository: Github.
Annotation of all Class I and Class II elements.
Data visualization in graphic format and phylogenetic trees.
A link with the results is sent 
Pre-computed Annotation Examples:
Click here
