Terrier Experimental Data
This repository contains the data for the application of Terrier to experimental data. See also: https://github.com/rbturnbull/terrier-experimental-data
There are 8 libraries of transposable elements (TEs) from flatworms. See the following directories:
- flatworms/Clonorchis_sinensis
- flatworms/Dicrocoelium_dendriticum
- flatworms/Fasciola_hepatica
- flatworms/Fasciolopsis_buski
- flatworms/Schistosoma_haematobium
- flatworms/Schistosoma_japonicum
- flatworms/Schistosoma_mansoni
- flatworms/Trichobilharzia_regenti
Schistosoma mansoni also has a FASTA file with 21 TEs annotated in the NCBI database.
There are 51 libraries of TEs from amphibians:
- amphibians/Allobates_femoralis
- amphibians/Ambystoma_mexicanum
- amphibians/Bombina_bombina
- amphibians/Bombina_variegata
- amphibians/Bufo_bufo
- amphibians/Bufo_gargarizans
- amphibians/Dendropsophus_ebraccatus
- amphibians/Discoglossus_pictus
- amphibians/Eleutherodactylus_coqui
- amphibians/Engystomops_pustulosus
- amphibians/Gastrophryne_carolinensis
- amphibians/Geotrypetes_seraphini
- amphibians/Glandirana_rugosa
- amphibians/Hyalinobatrachium_fleischmanni
- amphibians/Hyla_sarda
- amphibians/Hymenochirus_boettgeri
- amphibians/Leptobrachium_ailaonicum
- amphibians/Leptobrachium_leishanense
- amphibians/Leptodactylus_fallax
- amphibians/Limnodynastes_dumerilii
- amphibians/Lithobates_catesbeianus
- amphibians/Lithobates_sylvaticus
- amphibians/Mantella_aurantiaca
- amphibians/Microcaecilia_unicolor
- amphibians/Nanorana_parkeri
- amphibians/Oophaga_pumilio
- amphibians/Oophaga_sylvatica
- amphibians/Pelobates_cultripes
- amphibians/Phrynoglossus_myanhessei
- amphibians/Phyllomedusa_bahiana
- amphibians/Pipa_carvalhoi
- amphibians/Pipa_parva
- amphibians/Platyplectrum_ornatum
- amphibians/Pleurodeles_waltl
- amphibians/Pseudophryne_corroboree
- amphibians/Pyxicephalus_adspersus
- amphibians/Rana_kukunoris
- amphibians/Rana_muscosa
- amphibians/Rana_temporaria
- amphibians/Ranitomeya_imitator
- amphibians/Rhinatrema_bivittatum
- amphibians/Rhinella_marina
- amphibians/Scaphiopus_couchii
- amphibians/Scaphiopus_holbrookii
- amphibians/Spea_bombifrons
- amphibians/Spea_hammondii
- amphibians/Spea_multiplicata
- amphibians/Staurois_parvus
- amphibians/Xenopus_borealis
- amphibians/Xenopus_laevis
- amphibians/Xenopus_tropicalis
Most amphibian repeat libraries were generated using RepeatModeler version 2.0.4 (excluding the LTR pipeline extensions by Jullien M. Flynn). Ambistoma mexicanum was generated using RepeatModeler version 2.0.5.
Each directory contains:
- a FASTA file with extension .fa with the library of TE sequences.
- a CSV file with the predictions from Terrier
- a plot comparing the Terrier predictions with the original annotations (XXXXXXX-comparison.png)
- a plot with the confusion matrix base on the original annotations (XXXXXXX-confusion.png)
A summary CSV of the results is found in `summary.csv`.
To reproduce the plot in the paper from the summary, run `plot-summary.py`. This script requires the same virtual environment as Terrier.
For more instructions, see: https://github.com/rbturnbull/terrier-experimental-data
Credits
Terrier was developed by:
If you use this dataset, cite the Terrier paper. See more information at: https://github.com/rbturnbull/terrier
Funding
Improving disease resilience in ecosystems using synthetic biology
Australian Research Council
Find out more...Increasing amphibian immunity to combat disease causing mass extinction
Australian Research Council
Find out more...History
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