Final answer:
To compare many genes in an organism, microarray analysis is the most suitable method as it allows for the simultaneous examination of thousands of genes, providing a holistic comparison between two samples and is particularly useful in research settings for studying gene expression in diseases and infections.
Step-by-step explanation:
The methods that should be used to compare many genes in an organism include several nucleic acid hybridization techniques such as microarray analysis, Southern blotting, and Northern blotting. However, to compare gene-expression patterns or to examine a multitude of genes at once, microarray analysis is the most appropriate and efficient technique.
Microarray analysis enables researchers to capture a comprehensive snapshot of gene expression by comparing two samples, such as cells infected with a virus versus uninfected cells, or cancerous cells versus healthy cells. DNA or cDNA fragments are immobilized on a chip and labeled with fluorescent dyes, allowing for concurrent observation of thousands of gene sequences or expression patterns, providing a clear advantage in large-scale genetic studies over techniques like Northern blotting, which detects mRNA, or Southern blotting, which identifies DNA. Although it requires expensive equipment and software for data analysis, it is pivotal in research settings for understanding diseases like cancer or infections.