Bioinformatics
Bioinformatics is the application of information technology to the management and analysis of biological data with the aid of computers.
Bioinformatics can be divided into 3 major divisions: 1) DNA/RNA, 2) Protein 3) Genome and 4) Metabolomics.
Genomics forcuses on the structure, function, evolution, mapping and editing of information in an organism’s DNA. Epigenetics looks at how cells control gene activity through processes like DNA methylation. Transcriptomics studies the complete set of RNA transcripts produced by a genome. Proteomics explores protein expression to understand cellular phenotypes and function. In this respect, Next-generation sequencing (NGS) technologies have revolutionized the understanding of the genome, epigenome, transcriptome and proteome. These cell “omics” can differ substantially within a microenvironment, even between cells that express the same biomarkers. Single-cell analysis explores tissue hterogeneity by studying the genome, epgenome, transcriptome or proteme of a single cell. Multiomics has also been critical to provide researchers with unprescendented potential to understand why different patients with the same type of cancer have variable responses to the same treatment. Understanding how genes and proteins are modulated differently in the rpesence of an infeciton provides unique insights into how the host immune system responds to pathogens and could to the discovery of druggable targets. (“multiomics: An overview of useful methods and applications: harness the power of studying multiple “omes” in one experiment. Illumina. 2022).
Nucleic acid and Protein Sequences
There are many databases that can be used to compare protein and nucldic acid sequences. A helpful list of these databases is listed on the USPTO website.
Some of the commonly listed website are the following
Expasy (databses and toools for protein engineerin)
Peptide Synthesis
Companies: Sigma Genosys
Peptides can be designed de novo, but most peptides of biological interest are derived from N-terminal, C-erminal, or internal sequences of native proteins. Unfortunately, there are valid reasons why certain native sequences soemtimes need to be altered. Even for relatively short sequences, there are essential and non-esstial amino acid residues, although the relative importance of the individual amino acid residues is not always easy to determine. The “not-so-straighforward” rule of thum is to make the changes in the non-essential residues. These changes may include amino acid substitution (e.g., for solubility, stability, etc), chemical modification(e.g., for stability, structure-fuciton sutides), attachmet of ligands and conjugation. (SIGMA “Designing custom peptides” 2004, pp. 1-2).