Abstract
Publisher Summary This chapter describes the merits of several basic analysis and annotation paradigms available to the user within the Gene Relationships Across Implicated Loci (GRAIL) and genQuest tool suite, ranging from totally automated processing to the interactive analysis of large genomic regions. It also demonstrates what biological insights can be gained or missed in the analysis of several types of DNAs. The tools and techniques that are discussed aid in this analysis by identifying biologically relevant features in the sequence, and the chapter provides some insight into their potential function. With modest effort, an investigator can greatly enrich the value of the sequence under study by including descriptions of the genes, proteins, and regulatory regions that are present. Such analysis will provide a starting point to this most exciting phase of genome research. Constructing GRAIL has also required consideration of many practical issues related to users and useful analysis procedures.
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