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Table 1 Tools and databases used to annotate TEs in the genomes of multicellular eukaryotes published in 2014

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]

  1. aNot all tools used in building TE libraries are listed (e.g., UCLUST, MUSCLE)