Over time, we will capture sample protocols for the analysis of Transposable Elements.
The tables below provide links to protocol papers and open workshop resources, but can be also linked to resources uploaded on TE Hub.
Currently, two tables distinguish Bioinformatic and Molecular Biology protocols.
| Protocol name | Programs | TE analysis | TE type | Protocol link | Model(s) | Year |
|---|---|---|---|---|---|---|
| Curation Guidelines for de novo Generated Transposable Element Families | alignAndCallConsensus, ClusterPartialMatchingSubs, AutoRunBlocker | curation, subfamily analaysis | all TE | Storer et al. 2021 | Mammalia | 2021 |
| Mining of Miniature Transposable Elements in Brassica Species at BrassicaTED | BrassicaTED | database search | MITE | Jayakodi et al., 2021 | Plants, Brassica | 2021 |
| Bioinformatics Analysis Guides to LTR Retrotransposon-Derived Extrachromosomal Linear DNAs Identified by ALE-seq | ALE-seq | high-throughput identification of novel LTR | LTR | Wang et al., 2021 | Plants | 2021 |
| Detection of Transposition Events from Next-Generation Sequencing Data | TIF | insertion polymorphism | All TE with TSD | Miyao 2021 | --- | 2021 |
| Efficient Detection of Transposable Element Insertion Polymorphisms Between Genomes Using Short-Read Sequencing Data | SPLITREADER, TEPID | insertion polymorphism | all TE | Baduel et al., 2021 | Plants | 2021 |
| Detecting Signatures of TE Polymorphisms in Short-Read Sequencing Data | Detettore | insertion polymorphism | all TE | Stritt et al., 2021 | Plants, Brachypodium | 2021 |
| A Predictive Approach to Infer the Activity and Natural Variation of Retrotransposon Families in Plants | LTRpred | functional annotation | LTR | Benoit et al., 2021 | Plants | 2021 |
| In Silico Identification of Stress-Associated Transposable Elements in Arabidopsis thaliana Using Public Transcriptome Data | StringTie, edgeR | differential expression | all TE | Doğa et al. 2021 | --- | 2021 |
| A Tutorial of EDTA: Extensive De Novo TE Annotator | EDTA | de novo repeat identification from genome assembly | all TE | Su et al. 2021 | --- | 2021 |
| Global analysis of repetitive DNA from unassembled sequence reads using RepeatExplorer2 | RepeatExplorer2 | in silico repeat identification by read clustering | all TE | Novák et al. 2020 | --- | 2020 |
| Automatic annotation of transposable elements in a genome assembly | RepeatModeler2, RepeatMasker | de novo repeat identification from genome assembly | all TE | online tutorial | --- | 2021 |
| Earl Grey: Automatic de novo annotation of transposable elements in a genome assembly | Earl Grey | de novo repeat identification and curation from genome assembly, including summary plots | all TE | github:TobyBaril | --- | 2021 |
| Protocol name | Method name | TE analysis | TE type | Protocol link | Model(s) | Year |
|---|---|---|---|---|---|---|
| Detection of Transposable Element Insertions in Arabidopsis Using Sequence Capture | Sequence Capture | insertion polymorphism | all TE | Quadrana et al., 2021 | Plants, Arabidopsis | 2021 |
| Genome-Wide Identification of Miniature Inverted-Repeat Transposable Elements by Targeted High-Throughput Sequencing | targeted high-throughput sequencing | MITE | Tang et al., 2021 | Plants, Rice | 2021 | |
| Identification of Extrachromosomal Circular Forms of Active Transposable Elements Using Mobilome-Seq | Mobilome-Seq | active DNA transposons and retrotransposons | Extrachromosomal Circular TE | Tang et al., 2021 | Plants | 2021 |
| Identification of Active Transposable Elements in Plants: The Mobilome-Seq Approach | Mobilome-Seq | active DNA transposons and retrotransposons | Retrotransposons | Thieme et al., 2021 | Plants | 2021 |
| High-Throughput Profiling of Extrachromosomal Linear DNAs of Long Terminal Repeat Retrotransposons by ALE-seq | ALE-seq | high-throughput identification of novel LTR | LTR | Wang et al., 2021 | Plants | 2021 |
| Determination of TE Insertion Positions Using Transposon Display | Transposon Display | insertion polymorphism | Retrotransposons | Kim et al., 2021 | Plants | 2021 |
| Quantitative Measurement of Transposon Copy Number Using the Droplet Digital PCR | ddPCR | copy number variation | Retrotransposons, EVADE | Fan et al., 2021 | Plants, Arabidopsis | 2021 |
| Measurement of Genetic Mobility Using a Transposon-Based Marker System in Sorghum | TE-TRAP | PCR-based marker | PIF/Harbinger | Stritt et al., 2021 | Plants, Sorghum | 2021 |
| Sequence-Specific Amplified Polymorphism (SSAP) and Sequence Characterized Amplified Region (SCAR) Markers in Zea mays | Sequence-specific amplified polymorphism (SSAP), Sequence characterized amplified region (SCAR) | insertion polymorphism | LTR | Roy et al., 2021 | Plants, Maize | 2021 |