Table 2

Sequence and gene family discovery rates for various complete and partial genome datasets


Sequence rate (%)†
 Family rate (%)†


Dataset*
 No. of complete/partial genomes
 OSDR
 CSDR
 OGDR
 CGDR
CG Archaea
 19
 37.8
 -
 38.7
 -
CG Bacteria
 161
 19.5
 11.8 (± 1.5)
 22.4
 15.4 (± 1.8)
CG Bacteria strains filtered
 127
 28.4
 15.9 (± 1.5)
 26.6
 20.6 (± 1.7)
CG Bacteria
 127
13.4 (± 1.7)
17.0 (± 2.0)
CG Bacteria species filtered
 86
 23.2
 20.9 (± 1.6)
 31.5
 26.1 (± 1.6)
CG Bacteria
 86
16.3 (± 1.8)
19.9 (± 2.1)
CG Eukarya
 19
 39.0
 -
 30.8
 -
PG All
 193
 53.7
 40.3 (± 2.9)
 47.7
 42.8 (± 2.8)
PG Arthropods
 16
 74.7
 -
 66.4
 -
PG Deuterostomes
 21
 71.7
 -
 60.8
 -
PG Fungi
 27
 70.2
 -
 60.2
 -
PG Nematodes
 31
 62.8
 -
 47.0
 -
PG Protists
 17
 88.1
 -
 71.5
 -
PG Viridiplantae
 76
 48.3
 -
 37.8
 -
CG Bacteria sequences > 100 residues
 161
 -
 8.6 (± 1.4)
 -
 -
PG Sequences > 300 bp
 193
 -
 35.6 (± 2.8)
 -
 -

*CG, complete genome datasets; PG, partial genome datasets; 'strains filtered' indicate that only a single species representative was included in the analysis; 'species filtered' indicate that only a single genus representative was included in the analysis. †OSDR, overall sequence discovery rate (the total number of distinct sequences/total number of sequences); CSDR, current sequence discovery rate (obtained from Figure 1d, e); OGDR, overall gene family discovery rate (total number of families/total number of sequences); CGDR, current gene family discovery rate (obtained from Figure 1d, e).

Peregrín-Álvarez and Parkinson Genome Biology 2007 8:R238   doi:10.1186/gb-2007-8-11-r238

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