On The Origin Of A Genetic Constant - 10

Fig. 1 No Signal? Just Noise?

I. Introduction

In the previous post of this series some basic details about how the ~(32/35/25/6) DNA constant is calculated were presented (On The Origin Of A Genetic Constant - 9).

In today's post the work of the software that processes GenBank genomes is detailed, which hopefully makes understanding the entire 'constant' concept easier.

The appendix (Appendix One) contains multiple examples of the results of the software's processing of GenBank fasta files that are composed of sequences of genomes of various organisms.

The purpose of this series is to "paint a picture on a puzzle", i.e. to help us all to be able to paint a picture of the atomic dynamics of DNA genomes on top of that ubiquitous puzzle.

II. Difficulties

While a jigsaw puzzle like the example in Fig. 1 can be solved even if it is picture-less ,  it can be solved orders of magnitude more easily if there is a picture on it.

The "jigsaw puzzle" the ~(32/35/25/6) DNA constant presents does not have a "picture" on it when we take a look at the atomic structure of genomes.

For just one thing, that is because only 4 atom types are involved in any 'A', 'C', 'G', and 'T' nucleotide within those DNA genomes, and to make things even more picture-less, those 4 atom types follow a constant configuration, i.e. the ~(32/35/25/6) DNA constant.

III. The Jigsaw Pieces

The appendix has several sections as follows:

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Fig. 2 (about those software results in the appendix)

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Genbank File Genome link: a link to the GenBank organism data.

Source: the taxonomic name of the organism

ACGT Nucleotide Counts:

Adenine ('A') count: number of 'A' nucleotides
Cytosine ('C') count: number of 'C' nucleotides
Guanine ('G') count: number of 'G' nucleotides
Thymine ('T') count: number of 'T' nucleotides

Valid Nucleotide content: total number of valid ACGTs
Invalid Nucleotide content: total number of invalid values

Atom content:

Total Atoms: total number of atoms in the valid ACGTs
Atoms Per Nucleotide: average number of atoms per nucleotide

ACGT Atom Percents:

Adenine ('A'):

percentage list of atoms in the genome sequence

Cytosine ('C'):

percentage list of atoms in the genome sequence

Guanine ('G'):

percentage list of atoms in the genome sequence

Thymine ('T'):

percentage list of atoms in the genome sequence

Atom percent sums:

Carbon: total percent and (section-percent-list of atoms)
Hydrogen: total percent and (section-percent-list of atoms)
Nitrogen: total percent and (section-percent-list of atoms)
Oxygen: total percent and (section-percent-list of atoms)

Total percent: sum of atom types

Atom variation from ~(32/35/25/6) constant:

Carbon: percent of variation from the constant percent
Hydrogen: percent of variation from the constant percent
Nitrogen: percent of variation from the constant percent
Oxygen: percent of variation from the constant percent

        (note: a '<' means less than a constant; a '>' means more than)

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Once you look at the 'puzzle pieces' in the appendix, perhaps you can help other Dredd Blog readers to get the picture to cover the puzzle with.

The puzzle is "How do just 4 atom types do all the work of all the pieces of all the genetic puzzles of all the billions of organisms?"

The next post in this series is here, previous post in this series is here.

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