Rosalind algorithmic DNA challenges My python solutions for the Rosalind challenge, might be interesting for some people to see how I solved those, please don't use it to cheat. Will add some notes on what I found interesting while discovering the field through the AP Biology program of Khan Academy.

• Python 3
• Biopython library
• pygraphviz library
• networkx library

• http://www.bioinformatics.babraham.ac.uk/projects/download.html
• MEME suite http://meme-suite.org/index.html
• ORF Finder http://www.bioinformatics.org/sms2/orf_find.html
• EMBOSS http://emboss.sourceforge.net/what/
• LALIGN https://www.ebi.ac.uk/Tools/psa/lalign/

• E.coli bacteria: http://ecoliwiki.net
• C.elegans worm: http://www.wormbook.org/
• Virii: https://viralzone.expasy.org/

• Some types of non-coding RNAs (RNAs that do not encode proteins) help regulate the expression of other genes. Such RNAs may be called regulatory RNAs. For example, microRNAs (miRNAs) and small interfering RNAs siRNAs are small regulatory RNA molecules about 22 nucleotides long. They bind to specific mRNA molecules (with partly or fully complementary sequences) and reduce their stability or interfere with their translation, providing a way for the cell to decrease or fine-tune levels of these mRNAs.
• These are just some examples out of many types of noncoding and regulatory RNAs. Scientists are still discovering new varieties of noncoding RNA.
• Other kinds of regulatory RNA, such as long non-coding RNA (lncRNA) and piwi-interacting RNA (piRNA), have also been discovered, but their functions are not as well understood. There's growing evidence that miRNAs and other small, non-coding RNAs are involved in certain human diseases, including some genetic diseases and cancers. In addition, researchers are developing artificial microRNAs as therapeutic tools to treat human diseases. These are just a few examples of regulatory RNAs. There are many others, and more continue to be discovered over time. https://en.wikipedia.org/wiki/Piwi-interacting_RNA https://en.wikipedia.org/wiki/RasiRNA

• Seems like HOX genes are reading parts of lncRNA as "software inputs" to code for parts.
• Les genes HOX sont liés avec la polydactylie et visiblement les infos de croissance.
• L'inversion des HOX de la drosophile provoque la poussée de pattes à la place des antennes.
• Lien avec la grammaire du vivant "Splice"
• Les tardigrades ont des spécificités HOX https://fr.wikipedia.org/wiki/G%C3%A8ne_Hox
• https://www.franceinter.fr/emissions/la-tete-au-carre/la-tete-au-carre-19-mai-2011 (10mn40) https://fr.wikipedia.org/wiki/Denis_Duboule https://genev.unige.ch/fr/research/laboratory/Denis-Duboule
• En particulier, nous nous intéressons à la fonction possible de LncRNAs produits au sein des clusters Hox et proposés par d’autres laboratoires comme étant essentiels pour la fonction et la régulation des gènes Hox. Dans ce contexte particulier, ces études sont ciblées sur les ébauches des membres et le tractus intestinal.
• http://acces.ens-lyon.fr/acces/thematiques/evolution/relations-de-parente/comprendre/genes-homeotiques-hlg
• Les genes HOX sont responsable des rayures des guepes (max 10 genes HOX).
• 40 genes HOX chez les vertebres.
• Lien entre penis et doigts chez les genes architectes.
• Les genes HOX du serpent sont une boucle infinie.
• Les genes HOX sont coordonés visiblement. Pas de top gene architecte.

• https://en.wikipedia.org/wiki/Homeobox
• Use of https://en.wikipedia.org/wiki/Helix-turn-helix who is universal and binds to DNA.

http://www.cours-de-biochimie.fr/operons.php

• Allosteric means remote action
• They seem to act like timed logic gates OR | AND
• Allosteric inhibition: if A not B
• Allosteric activation: if A, B
• Michaelis-Menten enzymes with a switch state.

https://en.wikipedia.org/wiki/Luciferase

• The usage of multiple reading frames leads to the possibility of overlapping genes; there may be many of these in virus, prokaryote, and mitochondrial genomes.[7] Some viruses, e.g. Hepatitis B virus and BYDV, use several overlapping genes in different reading frames.

• Deletion
• Duplication
• Translocation
• Inversion
• Insertion
• Ring (boite a musique)
• Isochromosome

• Equilibrium relations can smoothen pH variations to a stable level.
• Acts a an int(pH).

https://en.wikipedia.org/wiki/DNA_methylation

• C & A can be methylated.
• Strengthens this specific pair.
• Blocks
• Similar to escaping SQL filters.

https://en.wikipedia.org/wiki/Mitochondrion

• Synteny blocks appear close to coding blocks or functions.
• Synteny blocks are very similar areas of two species genomes that have been flipped and moved around by rearrangements.

• KEGG pathways are fascinating.
• Optimal pathways can be found using shortest paths in a DAG with energy weights using bellman_ford_path_length applied to pathways. https://mriduls-networkx.readthedocs.io/en/latest/reference/algorithms/generated/networkx.algorithms.shortest_paths.weighted.bellman_ford_path_length.html#networkx.algorithms.shortest_paths.weighted.bellman_ford_path_length
• Is linked to the topological sorting in graph theory https://networkx.github.io/documentation/stable/reference/algorithms/generated/networkx.algorithms.dag.topological_sort.html?highlight=topological#networkx.algorithms.dag.topological_sort

Because transversions require a more drastic change to the base's chemical structure, they are less common than transitions. Across the entire genome, the ratio of transitions to transversions is on average about 2. However, in coding regions, this ratio is typically higher (often exceeding 3) because a transition appearing in coding regions happens to be less likely to change the encoded amino acid, particularly when the substituted base is the third member of a codon (feel free to verify this fact using the DNA codon table). Such a substitution, in which the organism's protein makeup is unaffected, is known as a silent substitution.

• Different regions of the genome evolve in different ways. In coding regions, where any significant change can be lethal to the organism, the most common source of variation is point mutations. In non-coding regions (introns or intergenic spacers), we find a different situation: entire intervals can easily be duplicated, inserted, deleted, or reversed.
• Transposons are jumping genes in non-coding DNA
• Mobility of "variables" non-coding transposons
• Inter specie transposons is fascinating. https://en.wikipedia.org/wiki/Tn10

• Controlled environment in the scientific method destroy the ecosystem complexity.

Tale of us, Stephan Bodzin, Hidden Empire, Matador, Guy J, Dale Middleton