Table 4 |
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|
Mean percentage amino acid identity of OMZ 50-m reads with top matches to distinct reference databases (GOS, KEGG, NCBI-nr) and with ribosomal proteins removed |
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|
Percentage identity to reference genes present inb |
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|
|
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|
Databasea |
Data |
DNA+RNAc |
DNA onlyd |
RNA only |
Alle |
|
|
|
||||||
|
All data |
||||||
|
GOS |
DNA |
89.3 |
82.1 |
NA |
82.8 |
|
|
GOS |
RNA |
90.8 |
NA |
87.5 |
89.3 |
|
|
KEGG |
DNA |
67.8 |
58.3 |
NA |
59.7 |
|
|
KEGG |
RNA |
71.0 |
NA |
69.4 |
69.6 |
|
|
NR |
DNA |
71.0 |
59.8 |
NA |
60.8 |
|
|
NR |
RNA |
73.8 |
NA |
72.2 |
72.7 |
|
|
Without ribosomal proteinsf |
||||||
|
NR |
DNA |
70.7 |
59.6 |
NA |
60.6 |
|
|
NR |
RNA |
73.6 |
NA |
71.9 |
72.5 |
|
|
|
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|
aBLAST database against which reads were compared. bMean percentage identity across all genes identified via BLASTX against NCBI-nr (HSP alignment regions only; bit score cutoff = 50). cGenes present in both DNA and RNA datasets, that is, 'expressed' genes. dGenes present only in the DNA dataset, that is, 'non-expressed' genes. eGenes shared between datasets (in DNA + RNA) plus genes unique to a dataset. fRibosome-associated proteins removed manually from datasets. BATS, Bermuda Atlantic Time Series; BLAST, Basic Local Alignment Search Tool; GOS, Global Ocean Sampling; HOT, Hawaii Ocean Time Series; HSP, high-scoring segment pair; KEGG, Kyoto Encyclopedia of Genes and Genomes; NA, not applicable; NR, National Center for Biotechnology Information non-redundant protein database (NCBI-nr); OMZ, oxygen minimum zone. |
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|
Stewart et al. Genome Biology 2011 12:R26 doi:10.1186/gb-2011-12-3-r26 |
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