From DNA to XNA: Adding STRINGS to Human Genome A DNA molecule is made of six strings to form a hexagonal shape. Remote gene editing capabilities are a reality via AI and the manipulation of our light (our biophotons), electro-magnetism (our electrons) and mechanical vibrations (SOUND i.e the Nth octave; the QUANTUM) using biological circuits, DNA logic gates, synthetic photonic crystals, and quantum dots embedded in nanoscale semiconductors. These are Real-Time Operating Systems (RTOS) that can be used for digital signals processing. In 2013 the SCOTUS decision in the Myriad Genetics case clarified that cDNA is patentable because it does not occur in nature. DNA -> cDNA -> XNA Biostrings Efficient manipulation of biological strings Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences. bioconductor.org/packages/re… GenomAutomorphism This is a R package to compute the automorphisms between pairwise aligned DNA sequences represented as elements from a Genomic Abelian group. In a general scenario, from genomic regions till the whole genomes from a given population (from any species or close related species) can be algebraically represented as a direct sum of cyclic groups or more specifically Abelian p-groups. Basically, we propose the representation of multiple sequence alignments of length N bp as an element of a finite Abelian group created by the direct sum of homocyclic Abelian group of prime-power order. bioconductor.org/packages/re… pwalign Perform pairwise sequence alignments The two main functions in the package are pairwiseAlignment() and stringDist(). The former solves (Needleman-Wunsch) global alignment, (Smith-Waterman) local alignment, and (ends-free) overlap alignment problems. The latter computes the Levenshtein edit distance or pairwise alignment score matrix for a set of strings. bioconductor.org/packages/re… Quasispecies Diversity QSUtils is a set of utility functions intended for use with viral quasispecies amplicon NGS data, but it could also be useful for analyzing 16S/18S ribosomal-based metagenomics or tumor genetic diversity by amplicons. Most functions are equally useful for metagenomic studies. There are three main types: (1) data manipulation and exploration—functions useful for converting reads to haplotypes and frequencies, repairing reads, intersecting strand haplotypes, and visualizing haplotype alignments. (2) diversity indices—functions to compute diversity and entropy, in which incidence, abundance, and functional indices are considered. (3) data simulation—functions useful for generating random viral quasispecies data. bioconductor.org/packages/re… I FOUND IT Y'all the XNA is REAL!!! ⚠️ XNAString ⚠️ Efficient Manipulation of Modified Oligonucleotide Sequences The XNAString package allows for description of base sequences and associated chemical modifications in a single object. XNAString is able to capture single stranded, as well as double stranded molecules. Chemical modifications are represented as independent strings associated with different features of the molecules (base sequence, sugar sequence, backbone sequence, modifications). It also enables secondary structure prediction using RNAfold from ViennaRNA. XNAString is designed to be an efficient representation of nucleic-acid based therapeutics, therefore it stores information about target sequences and provides an interface for matching and alignment functions from Biostrings and pwalign packages. ⚠️ XNAString is able to capture single stranded oligonucleotides, siRNAs, PNAs, shRNAs, gRNAs and synthetic mRNAs, and enable users to apply sequence-manipulating Bioconductor packages to their analysis. XNAString can read and write a HELM notation, compute alphabet frequency, align and match targets. ⚠️ bioconductor.org/packages/re…

#Biyoinfo101 'de bu hafta Pairwise-Çoklu ve Lokal-Global dizi hizalamalarının üzerinden geçiyoruz! #dizihizalma #sequencealignment #pairwisealignment #multiplealignment #globalalignment #localalignment

Pairwise alignment between Humans and Chimps. If you compare DNA of two species letter by letter, you get close to 99% of matching similarity. #Evolution #Primate #PairwiseAlignment #Bioinformatics

🧵 Did you know that protein alignment is often more informative than DNA alignment? ⬇️ Here is why. #bioinformatics #alignment #pairwisealignment #proteinalignment #dnaalignment