Iconcept Press Genomics III: Methods, Techniques and Applications

Genomics is the study of the genomes of organisms. The field includes intensive efforts to determine the entire DNA sequence of organisms and fine-scale genetic mapping efforts. It is a discipline in genetics that applies recombinant DNA, DNA sequencing methods, and bioinformatics to sequence, assemble, and analyse the function and structure of genomes. Genomics III - Methods, Techniques and Applications is the last volume of our Genomics series. Chapter 1 presents an overview of exome sequencing technology and details its use in identification of molecular bases of rare diseases in human. Chapter 2 describes and compares different methods of whole genome amplification (WGA) for replenishing DNA samples for genetic studies. Chapter 3 ilustrates the method of whole genome microarray gene expression profiling and its application to study the treatment effect of a widely used cardiovascular drug. Chapter 4 describes a brief history of large-insert libraries and their utility in exploring organisms with poor genetic and genome information. Chapter 5 proposes a bio-molecular approach for the evaluation of the anaerobic digestion performance. In Chapter 6, quantitative issues of the transposon-based gene delivery methods are addressed. Using the Sleeping Beauty transposon system as a prominent example, special detailed focus is given to copy number determination and to transposon excision efficiency quantification by real-time PCR based methodologies. Chapter 7 provides an overview of extraction of a compendium of sequence and structural features, as well as the methodology for function prediction based on the techniques from Artificial Intelligence and Machine learning. Chapter 8 presents a statistical method and a data mining solution for the problem of insertion site analysis and characterization of Alu elements Chapter 9 investigates how Mutual Information (MI) can be used to improve methods of predicting functional residues and enhance structural data to describe the topological properties of amino acid coevolution networks within a protein and their interactions. Chapter 10 attempts to validate MLVA to see if it could predict MRSA clones that were previously characterized by PFGE, MLST, and staphylococcal cassette chromosome mec (SCCmec) typing and to establish possible criteria of clustering MLVA patterns, looking for high concordance levels. Chapter 11 introduces a web server which allows the user to perform genome rearrangement analysis using reversals, block-interchanges (also called generalized transpositions) and translocations (including fusions and fissions). Chapter 12 discussed an algorithm which is used to optimally align simple sequence repeat (microsatellite) regions as they evolve uniquely through a process called polymerase slippage. Chapter 13 possesses a background of the RUN domain research with an emphasis on the interaction between RUN domain protein including RUFY proteins and small GTPases with respect to the cell polarity and membrane trafficking. In Chapter 14, the authors detail recent advances in understanding mechanisms of gene regulation in Drosophila. Chapter 15 provides guidelines for human molecular geneticists to perform genetic screenings using next generation sequencing. Chapter 16 describes the process that was used to locate and characterize small group I introns in the rRNA gene locus of fungi. Chapter 17 summarizes recent insights in the biology of variant gene transcription in human and murine malaria species and addresses the molecular mechanisms at work which regulate the expression of important virulence factors.