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Table 1 Overview and content of the TRAPID reference databases

From: TRAPID: an efficient online tool for the functional and comparative analysis of de novoRNA-Seq transcriptomes

Reference database

Functional annotation

Clade

#Species

#Proteins

Gene family information

OrthoMCL-DB version 5

PFAM domains

All

150

1,398,546

OrthoMCL clustering

  

Alveolata

15

98,796

 
  

Amoebozoa

4

41,930

 
  

Archaea

16

30,233

 
  

Bacteria

36

112,059

 
  

Euglenozoa

9

107,034

 
  

Eukaryota

98

1,256,264

 
  

Fungi

24

680,778

 
  

Metazoa

29

529,788

 

PLAZA 2.5

Gene Ontology, InterPro domains

Viridiplantae (green plants)

25

780,667

TribeMCL clustering + integrative orthologs

  

Angiosperms

18

671,950

 
  

Eudicots

13

480,106

 
  

Monocots

5

191,844

 
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Genome Biology

ISSN: 1474-760X

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