Genomic Databases and Softwares: In Pursuit of Biological Relevance through Bioinformatics

Abstract

With the completion of human genome project, a plethora of information had been available for exploring various unanswered questions related to cell and molecular biology. Bioinformatics has been instrumental in unravelling the genetic, phenotypic, structural and functional aspects of the whole genome by using this information. Genomics and proteomics have become one of the most relevant fields after the advancements in computational analysis, interpretation, and modelling software. It can not only quite categorically describe the position of nucleotides and amino acids throughout genomes and proteomes respectively, but it also helps in performing the phylogenetic analysis, search for associated transcription factors, multiple sequence alignments, and many other relevant explorations/hunts. The advances in the knowledge of genetics acquired from molecular biology and bioinformatics are applied and point towards potential therapeutic strategies such as genome editing. This review has an aim of discussing some of the bioinformatics databases and software, which has been utilized for exploring the position of a DNA sequence, any associated single nucleotide polymorphism (SNP) related to a disease, on or nearby situated transcription factor binding sites followed by multiple sequence alignment of this sequence with other organisms. This study provides the insights in to the functional elements of any DNA, RNA or Protein sequence prior to exploring the structural polymorphism, which may regulate the gene expression. Also, this review briefly discusses the tools used for programmable nuclease-based genome editing technology.

The Epigenetics of Psychosis: A Structured Review with Representative Loci

“…3 UTR-the untranslated region of mRNA that is 3 (downstream) to the translation stop site; 5 UTR-the untranslated region of mRNA that is 5 (upstream) to the translation start site; 5hmC-a cytosine that has first been methylated to form 5mC and then the methyl group is hydroxylated in a separate enzymatic step, regarded as part of the methylation reversal process. 5mC-a cytosine that has been methylated at the 5th carbon in cytosine, m C; aa-amino acid; AKT1-a serine/threonine phosphokinase (originally referred to as Protein Kinase B), leading to the phosphorylation of serine and threonine residues in specific proteins, important in signaling cascades; Alibaba2-a well-cited online program (cited by Kaushik et al [216] Whitaker and Ostrander, [217]; Haro et al [218]) that predicts transcription factor binding sites in a DNA sequence: http://gene-regulation. com/pub/programs/alibaba2/index.html (accessed on 1 November 2021); alpha-MSHalpha-melanocyte-stimulating hormone, a member of the melanotropin family of peptides; ASSP-Alternative Splice Site Predictor program: http://wangcomputing.com/assp/ (accessed on 1 November 2021); Augustus-an online program that predicts open reading frames (ORFs): http://bioinf.uni-greifswald.de/augustus/submission.php (accessed on 1 November 2021); B3-the vitamins niacin and nicotinamide; BAT-brown adipose tissue, important in thermoregulation; CEBP-CCAAT/enhancer binding protein a transcription factor that enhances the function of GREs; CEU-a collection of DNA from individuals descended from a mixed population of northern Europeans in Utah; CpG-a dinucleotide pair of the bases cytosine and guanine in a DNA strand, frequently a site of cytosine methylation to yield m C, i.e., 5mC; note that all CpG sites discussed in this review have associated SNPs, but unless specified otherwise in this review, all are too rare to be of relevance to psychosis; dbPTM database on protein post-translational modifications https://awi.cuhk.edu.cn/dbPTM/ (accessed on 1 November 2021); DRD2-one of the receptors for which dopamine is a ligand, in this case, the dopamine receptor-2; EMBOSS-an online tool hosted by the European Bioinformatics Institute https://www.ebi.ac.uk/Tools/seqstats/emboss_cpgplot/ (accessed on 1 November 2021); EWAS epigenome wide association study; FDR-p value that incorporates adjustment for the false discovery rate estimate; FEP-first episode psychosis patients; GRE-glucocorticoid response element, a nucleotide motif to which the glucocorticoid receptor protein binds; GSK3β-glycogen synthase kinase-3 β, a substrate for AKT1; when phosphorylated by AKT1-P, is inactivated; HCAR3-the hydroxycarboxylic acid receptor-3, responsive to niacin and carboxylic acids involved in lipid homeostasis in fat tissue; originally known as HM74; HM74-the human receptor originally identified as responsive to niacin; now also known as HCAR3; HNF-1-a transcription factor protein; among other regulatory functions, involved in affecting the expression of tyrosine hydroxylase; hnRNP-C-heterogeneous nuclear ribonucleoprotein C, a transcription factor that represses use of alternative 5 -cryptic acceptors; hnRNP-PTB-heterogeneous nuclear ribonucleoproteina transcription factor that represses use of alternative splicing 5 -cryptic acceptors, with the PTB designating its effector, polypyrimidine tract binding protein; IDO-indoleamine 2,3-dioxygenase, an enzyme that catalyzes the formation of kynurenine from tryptophan; iMethyl-website identifying location of cg probes http://imethyl.iwate-megabank.org (accessed on 1 November 2021); Ldpop-a website maintained by the National Cancer Institute that, among other things, enables determination of likely haplotypes for specific alleles: https://ldlink.nci.nih.gov/?tab=ldpop (accessed on 1 November 2021); MC5R-the melanocortin receptor-5, for which alph...…”