All posts by Wei-Yin Chen

3mers from synthetic genomes vs. 3mers from real genomes as viewed in Skittle

[wpdm_file id=6] [NOTE: it will give a security warning because Skittle is not recognized by virus software as being safe, so ignore the message. It might have to be unzipped after download depending on the browser. To run skittle, run the file “SkittleToo” NOT “Skittle.exe”.]
[wpdm_file id=7] [NOTE: It might have to be unzipped after download depending on the browser.]

Below are screen captures of the Skittle repeat map and 3mer display of a synthetic DNA designed to generate the theoretical maximum 3mer patterns. The cause of the maximum 3mer pattern is “ATG” repeated through out a hypothetical synthetic genome. Other repeated codons which would also give the theoretical maximum 3mers are:
“ATC”, “ACG”, “ACT”, “AGT”, “AGC”,
“CAG”, “CAT”, “CGA”, “CGT”,”CTA”, “CTG”,
“GAC”, “GAT”, “GCA”, “GCT”, “GTA”, “GTC”,
“TAC”, “TAG”, “TCA”, “TCG”, “TGA”, “TGC.

Nucleotide display set at 128bp:
atg 128

Nucleotide display set at 2048bp:
atg 2048

Continue reading 3mers from synthetic genomes vs. 3mers from real genomes as viewed in Skittle

Mission of BioLanguages Website

To explore the linguistic constructs found at the molecular and structural levels
of individual organisms and groups of organisms.

The discovery of the triplet DNA code was the first major step in relating biological systems to linguistic constructs. Since then, more features of biology have been seen to conform to linguistic constructs beyond the triplet DNA code.

This website reports and comments on developments related to biological languages.