Genomes and Genomics
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Genomes and Genomics

How are sequence maps of genomes produced? How is the information in the genome deciphered? What can comparative genomics reveal about genome structure and evolution? How does the availability of genomic sequence affect genetic analysis? These genome projects would make the clones and then make the sequence as an available public resources.

Genomic analysis takes that approaches of genetic analysis and applies them to the collection of global data sets to fulfill goals such as the mapping and sequencing of whole genomes and the characteristics of all transcripts and proteins. Genomic techniques require the rapid processing of large sets of experimental material, all dependent on extensive automation.

The key problem in compiling an accurate sequence of a genome is to relate short sequences reads to one another by sequence identity to build up a consensus sequence of an entire genome. It can be done straightforward regarding bacterial or archaeal genomes by aligning overlapping sequences from different sequence reads to compile the entire genome, because there are no to few DNA segments that are present in more than one copy of prokaryotes. But complex genomes are replete with such repetitive sequences. These repetitive sequences interfere with accurate sequence contig production. The problem is resolved either by whole genome shotgun sequencing including the use of paired end reads or by ordered clone sequencing. Order clone sequencing treats dispersed repetitive elements as unique in the context of a clone. Unlike WGS sequencing, clone by clone sequencing requires that a physical map be produced of the oriented and ordered clones.

Having a genomic sequence map provides the raw, encrypted text of the genome. The job of the bioinformatics is to interpret this encrypted information. For the analysis of gene products, computational techniques are used to identify open reading frames, and non-coding RNAs and then to integrate these results with available experimental evidence for transcript structures (cDNA sequences), protein similarities, and knowledge of characteristic sequence motifs.

Conservation of sequences among species is a reliable guide to identifying functional sequences in the complex genomes of many animals and plants. Comparative genomes can also reveal how genomes have changed and how the changes may relate to differences in physiology, anatomy, or behavior among species. In bacterial genomes, comparisons of pathogenic and nonpathogenic strains have revealed many differences in gene content that may contribute to pathogenicitiy.

Functional genomics attempts to understand the working of the genome as a whole system. Two key elements are the transcriptome, the set of all transcripts produced, and the interactome, the set of interacting gene products and other molecules that together enable a cell to be produced and to function. The function of individual genes and gene products for which classical mutations are not available can be tested through reverse genetics- done by targeted mutation or phenocopying. 

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