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Developing Bioinformatics Computer Skills by Cynthia Gibas, Per Jambeck

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Chapter 11. Tools for Genomics and Proteomics

The methods we have discussed so far can be used to analyze a single sequence or structure and compare multiple sequences of single-gene length. These methods can help you understand the function of a particular gene or the mechanism of a particular protein. What you're more likely to be interested in, though, is how gene functions manifest in the observable characteristics of an organism: its phenotype . In this chapter we discuss some datatypes and tools that are beginning to be available for studying the integrated function of all the genes in a genome.

What sets genomic science apart from the traditional experimental biological sciences is the emphasis on automated data gathering and integration of large volumes of information. Experimental strategies for examining one gene or one protein are gradually being replaced by parallel strategies in which many genes are examined simultaneously. Bioinformatics is absolutely required to support these parallel strategies and make the resulting data useful to the biology community at large. While bioinformatics algorithms may be complicated, the ultimate goals of bioinformatics and genomics are straightforward. Information from multiple sources is being integrated to form a complete picture of genomic function and its expression as the pheotype of an organism, as well as to allow comparison between the genomes of different organisms. Figure 11-1 shows the sort of flowchart you might create ...

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