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Briefly, using the complete collection of genes in the S. cerevisiae genome, we randomly selected 1,000 pairs and performed the same procedure of upstream region local alignment.
For each of the 69 candidate gene losses, one-to-one orthologous gene was searched between human and nine species using the complete collection of orthologous protein-coding genes (Ensembl).
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This analysis was also performed for all sequenced genomes belonging to the phylum Firmicutes and genus Clostridium using the complete sequenced microbial genome collection from the NCBI (http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi, accessed: 06/23/2011).
Quartz tube reactors were used to ensure the complete collection of gaseous products in pyrolysis process.
For these curves, 95% confidence intervals were calculated under the assumption that the entire dataset represented a sample from a larger pool; these intervals do not converge on the actual count at maximum N. We estimated species richness for the complete collection using the abundance-based Chao 1 estimator [ 27] and for the 2010 subcollection using the incidence-based Chao 2 estimator [ 28].
The complete collection was then used to construct the knowledge space for the POLSA model.
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