From: A call for benchmarking transposable element annotation methods
Genome | Homology-based | De novo | Pipeline | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Repbase | RepeatMasker | CENSOR | RepeatProteinMask | RepeatModeler | RepeatScout | PILER | LTR_FINDER | LTR_STRUC | MITE-Hunter | REPET | Other Databases | Other toolsa | Ref. | ||
Phalaenopsis equestris (tropical epiphytic orchid) | Plant (monocot) | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | [81] | ||||||
Cyprinus carpio (common carp) | Animal (bony fish) | ✓ | ✓ | ✓ | TEClass | [82] | |||||||||
Esox lucius (northern pike) | Animal (bony fish) | ✓ | ✓ | ✓ | Genbank, UniprotKB/SwissProt | Custom | [83] | ||||||||
Oryza glaberrima (African rice) | Plant (monocot) | ✓ | ✓ | ✓ | ✓ | MSU Repeats, custom (rice-specific) | Custom | [84] | |||||||
Callithrix jacchus (common marmoset) | Animal (primate) | ✓ | ✓ | [85] | |||||||||||
Gossypium arboreum (cultivated cotton) | Plant (dicot) | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | [86] | |||||
Nicotiana tabacum (common tobacco) | Plant (dicot) | ✓ | ✓ | TIGR, SGN (Solanaceae-specific) | [87] | ||||||||||
Glossina morsitans (tsetse fly) | Animal (insect) | ✓ | ✓ | ✓ | ✓ | Genbank | RECON, TARGeT | [88] | |||||||
Oncorhynchus mykiss (rainbow trout) | Animal (bony fish) | ✓ | ✓ | ✓ | ✓ | ✓ | E-inverted, Manual | [89] | |||||||
Tetrao tetrix (black grouse) | Animal (bird) | ✓ | ✓ | [90] | |||||||||||
Pinus taeda (loblolly pine) | Plant (gymnosperm) | ✓ | ✓ | ✓ | ✓ | ✓ | PIER 2.0 (conifer-specific) | Custom | [91] | ||||||
Spirodela polyrhiza (duckweed) | Plant (monocot) | ✓ | ✓ | MipsREdat, MIPS PlantsDB | Custom | [92] | |||||||||
Cynoglossus semilaevis (half-smooth tongue sole) | Animal (flatfish) | ✓ | ✓ | ✓ | ✓ | RepBase (for classification) | E-inverted, Custom | [93] | |||||||
Capsicum annuum L. and var. glabriusculum (cult. and wild peppers) | Plant (dicot) | ✓ | ✓ | ✓ | ✓ | ✓ | MSU repeats | [94] | |||||||
Capsicum annuum cv. CM334 (hot pepper) | Plant (dicot) | ✓ | ✓ | ✓ | [95] | ||||||||||
Anopheles sinensis (mosquito) | Animal (insect) | ✓ | ✓ | Efam (mosquito-specific) | [96] |