Description of the genome query for

2D Plots of ORF characteristics

A genome's ORFs can be plotted according to any of the following characteristics:

  1. ORF length, in amino acid residues.
  2. ORF product molecular weight, in Daltons.
  3. ORF logarithm of the product molecular weight.
  4. ORF mol% G+C.
  5. ORF mol% G+C, first codon position.
  6. ORF mol% G+C, second codon position.
  7. ORF mol% G+C, third codon position.
  8. ORF mol% A+G.
  9. ORF position, as annotated.
  10. ORF product isoelectric point (pI), predicted from the sequence.
  11. ORF product proportion of hydrophobic amino acids, these being Ala, Ile, Leu, Met, Phe, Pro, Trp, Val.
  12. ORF product percent net charge, computed as %(Arg+Lys)-(Asp+Glu)
  13. ORF BLASTP score with its best homolog in the other selected genome.
  14. how well the ORF product matches outside of taxonomic level 1 (e.g., Bacteria).
  15. how well the ORF product matches outside of taxonomic level 2 (e.g., Proteobacteria).
  16. how well the ORF product matches outside of taxonomic level 3 (e.g., gamma subdivision).
  17. how well the ORF product matches outside of taxonomic level 4 (e.g., Enterobacteriaceae).
  18. evolutionary scope.
  19. PDS analysis at 1.0e-5.

A few of these characteristics require further explanation:

(xiv - xvii): How well the ORF product matches outside of the genome's lineage, at the specified depth.

For instance, choosing taxonomic level 3 for Escherichia coli K12 would find the ORF's best match outside of the gamma subdivision of the Proteobacteria.

(xviii): Evolutionary scope.

Using the genomic distance matrix computed at a BLASTP cutoff e-value of 1.0e-5, we compute the evolutionary scope of an ORF's matches. For example, if an ORF from Mycoplasma genitalium matches one or more ORFs from Mycoplasma pneumoniae, Mycoplasma penetrans and Ureaplasma urealyticum, then that ORF's evolutionary scope is the mean distance between M. genitalium and these other three species.

(xix): PDS analysis.

What we have done is to determine how well correlated a gene's relationships to its orthologs in other species is to the genome's overall relationships to orthologous genes from other species. A low value indicates a "phylogenetically discordant sequence", or "PDS". A high value indicates that the gene's relationships track the genome's relationships well. Details of this analysis are available from:
Clarke et al. (2002) J. Bacteriol. 184, 2072-2080.

Example:

We may be interested in the relationship between a protein's predicted isoelectric point and its predicted hydrophobicity. Selecting the Bacillus subtilis genome, and plotting isoelectric point versus % hydrophibic amino acids, we generate a plot with three distinct clouds of points: a group of acidic proteins that are non-hydrophobic, a group of basic non-hydrophobic proteins, and a group of basic hydrophobic proteins. One may examine these groups of proteins in more detail by switching to the "Sorted ORFs" query.

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