1. 1.Transposable elements (TEs) are mobile genetic elements that can replicate themselves within the host genome. They provide insights into the mechanisms underlying genetic diversity, gene regulation, and the evolution of plant traits.
  2. 2.WebTE provides TE families sequences for multiple species. Users can view TE families of different species through the Browse link.
  3. 3.WebTE provides users with automated TE discovery and annotation (Online Annotation), which enables users to explore TE landscapes in genomes.
  4. 4.Furthermore, WebTE can analyse the interaction relationship between TEs and genes (Genes Analysis), bringing a new perspective for the cultivation of new epigenetic variation in species.
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Workflow of WebTE

If you need help with WebTE, please contact Kang Hu or Jianxin Wang.

Features of WebTE

TE Online Annotation

HiTE is used as a backend TE detection tool, which is developed by our group. The workflow of HiTE is shown in the figure below. HiTE is an accurate dynamic boundary adjustment approach for full-length TE detection and annotation in Genome Assemblies.

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For more information, please refer to https://github.com/CSU-KangHu/HiTE.


Genes Analysis

TEs can affect gene expression by influencing cis-regulatory elements. For example, a transposon located upstream of the promoter can change the color of mouse fur. In oil palm, a transposon located in a control flowering gene ultimately determines whether the plant produces fruits with high oil content. WebTE provides users with interaction analysis of TEs and genes sites.

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Browser TE Families

Statistics

Species TE Families
0 0

Curated Species Lineage

Open species viewer

Species

TEs Online Annotation

Click the button below to load the sample data:





1. Select/Input Species Name

Select Species Name
No suitable species? Try entering the species name

2. Select a mode and upload the data

Uploading Genome File: (support suffixes with fna, fasta and fa)



3. Optional input

Online Annotation Parameters:

(1) is plant (0/1)
(0/1)
(2) miu
(default: 1.3e-08)


Phylogenetic Relationships Analysis

Click the button below to load the sample data:





1. Select the TE annotation libraries (allow for multiple selections)



2. Select a super family and domain



Genes and TEs

1. Select a species

2. Relationships between genes and TEs

Explanation:

  • 1. Distance Search Field can filter records whose distance between Gene and TE is less than the input value (the threshold of distance is 1000).
  • 2. Gene Start Position and TE Start Position represent the start positions of this gene and TE in the chromosome, respectively.
  • 3. Click the jump button, and the visual display will automatically locate the exact position.
Loading ...

Search filter:


Jobs of Online Annotation

Tips:Check the checkbox before download



Phylogenetic Relationships Analysis

1.Select results of concern

Instruction:

  • 1. Each record in the table represents a phylogenetic tree analysis job.
  • 2. Select a job with the status finished, click the Analyse button at the bottom of the table.
  • 3. Phylogenetic tree and detailed lineage information of families generated by multiple species are displayed in the form of graphs and tables.


2. Phylogenetic Tree: (The construction of the phylogenetic tree will be terminated when too few families are detected)

3. Lineage of Families:

Explanation:

  • The following table shows the detailed mapping information between the identified LTRs and TE protein domains.


Relationships between TEs and genes

1.Select results of concern

Instruction:

  • 1. Select the job in finished status.
  • 2. Click the Analyse button to display the information of related Genes and TEs.


1.Browse

workflow

Note 1: Explore the curated species lineage within WebTE.
Note 2: Search for species of interest by scientific name.
Note 3: Download TE families file for the desired species, which can be directly used as a library input for genome annotation with RepeatMasker.
Note 4: Search for specific content of interest within the table of TE families.


2.Online Annotation

workflow

Note 5: Load a sample for online annotation submission.
Step 1: Choose a species, including the option to enter a custom species name if it is not available in our database.
Step 2: Proceed to the next step.


workflow

Step 3: Upload a genome assembly file with the extension fna, fasta, or fa. Drag and drop file upload is supported.
Step 4: Proceed to the next step.


workflow

Step 5: Customize optional parameters for online annotation. For example, use the "is plant" parameter to indicate whether the species is a plant. Use "1" for plant and "0" for non-plant species. The "miu" parameter defines the neutral mutation rate (per bp per year). If unsure, you can use the default parameters..
Step 6: Submit the task.
Step 7: Set the permissions of this task. If the task is set as private, you will need to provide your email to bind the task for subsequent verification.
Step 8,9: Proceed to the next steps.


workflow

Note 6: Search for online annotation tasks.
Note 7: Select a specific task. If the owner is not public, you may need to undergo email verification for authorization.
Note 8: Download the TE families file for your task.


3.Genes Analysis

workflow

Note 9: Search for species.
Note 10: Display the relationship between TEs and genes for the selected species.


workflow

Note 11: Set filtering conditions for displaying the relationship between TEs and Genes.
Step 12: Hide TE entries that are not associated with genes.
Step 13: Navigate to the corresponding location of the TE in the IGV below.


workflow

Note 14: Navigate to different positions within the genome.
Note 15: Click to view detailed information about the Gene and TE.


4.Clear authorizations

workflow

Note 16: Clear all permissions associated with the current user. For private TE online annotation tasks, you will need to undergo email verification again for subsequent access.


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(i) TEs online annotation(find more details).
(ii) Genes and TEs(find more details).


The first module aims to identify TEs from genomic data. The second module is used to study the interaction between TEs and genes.

License

Permission is granted to use the content on this website for academic purposes, including educational and research purposes. Commercial use of any materials from this website is strictly prohibited without prior written consent.

Contact Information

For inquiries regarding the use of materials for commercial purposes or any other permissions, please contact us using the information provided below.


School of Computer Science and Engineering
Central South University
Changsha, Hunan Province, P.R. China

Email1: (Kang Hu) kanghu@csu.edu.cn;
Email2: (Jianxin Wang) jxwang@mail.csu.edu.cn;