= Ribosomal RNA oligonucleotide cataloguing
<Ribosomal RNA oligonucleotide cataloguing> compares <organisms> through collections of short sequences obtained from <ribosomal RNA>. Instead of determining one complete modern sequence, investigators generated fragments, identified their sequences and compared which longer fragments were shared. The resulting catalog supplied molecular evidence about relationships beyond external appearance.
The 1977 <Carl R. Woese> and <George E. Fox> paper describes digestion of small-subunit <ribosomal RNA> with <ribonuclease T1>, followed by separation of the products using two-dimensional <electrophoresis>. Sequencing the resulting <oligonucleotides> produced a catalog characteristic of the examined material. Comparing catalogs helped establish the distinct position of the methanogenic organisms discussed in the paper. This was an RNA-fragment experiment, not a modern amplified-marker survey.<Phylogenetic structure of the prokaryotic domain: the primary kingdoms by Carl R. Woese and George E. Fox>[p.5089, Table1 legend: digestion, fingerprint separation, sequencing and catalog comparisons; Abstract and Discussion: phylogenetic interpretation]{ref}
The <RNA oligonucleotide association coefficient> used nucleotide counts in cataloged sequences of six or more residues:
$$
S_{AB}=\frac{2N_{AB}}{N_A+N_B}.
$$
Here $N_A$ and $N_B$ count nucleotides represented by the eligible fragments in the respective catalogs, while $N_{AB}$ counts those represented in their shared portion. It is therefore not simply the fraction of fragment labels found in common, nor the percentage identity of a complete aligned RNA.<Phylogenetic structure of the prokaryotic domain: the primary kingdoms by Carl R. Woese and George E. Fox>[p.5089, Table1 legend: definition of the association coefficient and hexamer-or-larger restriction]{ref}
For an original accounting example, let $N_A=40$, $N_B=60$ and $N_{AB}=25$. Then $S_{AB}=50/100=0.50$. A catalog with fewer recorded nucleotide residues can share the same amount of material while giving a different normalized comparison. Agreement in short fragments alone also need not imply identical full sequences.
The scientific advance was a reproducible molecular comparison usable across morphologically different microbes. Its interpretation still depended on the marker, sampling and method. A catalog similarity supplies evidence for analysis in <phylogenetics>, not a complete reconstruction of every <gene>, a direct date of divergence or a guarantee that two <organisms> have the same physiology.
Back to article page
