There are significant differences in the distributions of QIPP scores between orphan and non-orphan genes for many genomes and a trend for less well-conserved genes to have lower QIPP scores.
A predominance of STRs in introns has not been reported for many genomes before, except e.g. for fungi in [ 9].
Calculation of genome length and GC content is incorrect for many genomes.
Semi-automated informatic approaches that are now being applied to all nematode sequences [ 55] allow uniform comparisons across many genomes and provide databases for further exploration.
We examined Dethlefsens and Schmidt's ΔN'c [ 46], Rocha's ENCdiff [ 10], and Sharp's S [ 8], but excluded von Mandachs and Merkl's GCBeff [ 13]because it cannot be meaningfully calculated for many genomes.
The survey also shows that although GOA-assigned predictions are the most comprehensive source of functional information for many genomes, a large proportion of genes in a variety of different organisms entirely lack these predictions but do have manual annotations.
Recently, many genomes have been sequenced primarily for their comparative analytic value (Green, 2007; Margulies and Birney, 2008; Margulies et al., 2005; Stark et al., 2007).
With the rapid accumulation of sequence data from many genomes, computational methods are needed for accurate prediction of DNA-binding residues in protein sequences.
Our approach bears the potential for universal applications and will play an important role in sequencing, mapping, and assembly of many large genomes for biomedical and agricultural purposes.
Because there were too many bacterial genomes for enrichment analysis and result presentation, archaeal genomes were chosen to showcase the differentiation at the phylum and family levels (see Additional file 7).
