Chimera Detection - 2

Where da chimera at?

I. How To

This post explains an easy way to peruse the appendices posted in the first episode of this series, beginning with the first appendix.

In the Firefox Web Browser (or compatible browser);

1) Follow the link to (Chimera Detection - Appendix 1);

2) Press "Ctrl F" and type "NC_000003.12" in the search-box that appears;

3) Notice that the first instance is located at "Full Genome Table: 2" where the details include "Nucleotide count: 198,100,135; 'N' Nucleotide Count: 195,424";

4) Press the down arrow associated with the search-box to go to the next instance of "NC_000003.12" which is located at "Promoter-Terminator Genes Table: 2 (Gene Count: 32)" where the details include "Nucleotide count: 82,163" (i.e. the total number of nucleotides in all of the 32 genes/TATA Box); (note that a promoter is "TATAAA" and a terminator is "TATCTC");

5) press the down arrow again to go to the next instance of "NC_000003.12" which is located at "Cleaned Genes Table: 2 (Gene Count: 32)" where the details include "Nucleotide count: 82,162; 'N' Nucleotide Count: 1";

6) Notice that when my software isolated then parsed each of the 32 genes/TATA Boxes it found a gene/TATA Box containing a nucleotide that was not a part of any valid standard codon;

Thus, one of the TATA Box and/or gene areas is chimeric, and that should be an issue:

"The FDA, in its response to a lawsuit filed by the Center for Food Safety in 1998, admitted in court that it had made “no dispositive scientific findings,” whatsoever, about the safety of genetically engineered foods.  In other words, the FDA has given the biotech industry carte blanche to produce and market any number of genetically engineered foods without mandatory agency oversight or safety testing and without a scientific showing that these foods are safe to consume."

(GE Food & Your Health). Perhaps both meat and vegetable genomes should be considered?

II. Explanation

The results are uniform when the genome and genes/TATA Box/transcription areas have standard codons, such as the "NC_000015.10" genome, however, the results vary when a chimeric status ensues.

Sometimes the "Promoter-Terminator Genes Table" and/or the "Cleaned Genes Table" are omitted because there was no promoter-terminator pair (TATA Box) in the genome.

III. Closing Comments

The discovery of the ~(32/35/25/6) fingerprint pattern in DNA which I announced in Dredd Blog post Quantum Biology - 22 is simple enough to use in a sophisticated word processor.

But since that is very tedious I may publish the software in a future post here on Dredd Blog.

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

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