Gene prediction is a comprehensive algorithm that deals with gene modeling, upstream modeling, start site initiation and overlapping genes issues. Despite the need for accurate gene prediction in prokaryotes, little effort has been dedicated to the comparison of various modeling strategies. This article...
Gene prediction inprokaryotes(Bacteria and Archaea) involves fewer confounding factors than in eukaryotes because in prokaryotes thegenome sizeis small and gene density is high, with ~88% of the genome containing coding sequences.11Bacteria do not have introns (Archaea have introns in rRNA and tRNA...
Experimental techniques for identification of essential genes (EGs) in prokaryotes are usually expensive, time-consuming and sometimes unrealistic. Emerging in silico methods provide alternative methods for EG prediction, but often possess limitations in
This observation suggests that autoregulation may be more prevalent in prokaryotes, whereas more complex circuitry has evolved in eukaryotes. Comprehensive physical and regulatory datasets in more complex multicellular organisms will provide further insights into the prevalence of autoregulation in the ...
Gene duplication is a normal evolutionary process. If there is no selective advantage in keeping the duplicated gene, it is usually reduced to a pseudogene and disappears from the genome. However, some paralogs are retained. These gene products are likel
Expression of most, if not all, genes in prokaryotes and eukaryotes occurs in a discontinuous fashion, involving episodes of activity separated by refractory intervals of complete or near-complete inactivity. In metazoans, this pulsatile nature of gene expression, dubbed transcriptional bursting, may be...
Many current gene prediction methods use only one model to represent protein-coding regions in a genome, and so are less likely to predict the location of genes that have an atypical sequence composition. It is likely that future improvements in gene fin
Chapter 6 Gene Prediction: Finding Genes in the Human Genome Figure 6.1: Map of the human X-chromosome Figure 6.2: Schematic view of a typical prokaryotic gene and the mRNA transcribed from the gene Figure 6.3: Transcriptional units in prokaryotes (A) can contain multiple open reading frames; ...
Despite the increasing accuracy of gene prediction tools there likely exists a large number of spurious protein predictions in the sequence databases. We have developed the Spurio tool to help identify spurious protein predictions in prokaryotes. Spurio searches the query protein sequence against a ...
Chlamydiae is a bacterial phylum composed of obligate animal and protist endosymbionts. However, other members of the Planctomycetes–Verrucomicrobia–Chlamydiae superphylum are primarily free living. How Chlamydiae transitioned to an endosymbiotic lifes