Comparison of DNA and mRNA from samples from mid- and post-phytoplankton bloom.

Size, clustering and annotation data were generated by CAMERA. rRNA and subsystem hits were generated by SEED.
aAnalysis of sequences against the Ribosomal Database Project II (RDP-II) and the European Ribosomal large subunit (LSU)dataset.
bBased on clustering at 95% identity over 80% length of a sequence and over 120 bp.
cFor direct comparison of samples, individual rarefaction analysis, by R (http://www.r-project.org/) and the vegan package (http://cc.oulu.fi/jarioksa/softhelp/vegan.html), was used to estimate the number of clusters in each sample after adjusting sample size of each dataset to be equivalent to the number of reads in the smallest dataset (mRNA – High CO2).
dPartial Open Reading Frames (pORFs) from six reading frame translation from all reads using translation table 11, starting at the beginning of a read or first ATG after previous stop codon, ending at the end of a read, or at a stop codon and being at least 30 contiguous amino acids.
eTotal pORF reads clustered at 95% identity of over 80% length of sequences.
fClusters are identified using the representative sequences of each cluster from the 95% step to cluster at 60% identity of over 80% length of sequences.
gThe dominant clusters (≥10 non-redundant sequences) with the exclusion of spurious pORFs.
hProtein families database.
iThe Institute for Genomic Research protein database.
jNCBI clusters of orthologous groups database.
kWith ≥10 non-redundant clustered sequences excluding spurious ORFs.
n/a – not analyzed.