Genomics: Genome-wide Analysis of Gene Structure and Expression
■ The function of a protein that has not been isolated often can be predicted on the basis of similarity of its amino acid sequence to proteins of known function.
■ A computer algorithm known as BLAST rapidly searches databases of known protein sequences to find those with significant similarity to a new (query) protein.
■ Proteins with common functional motifs may not be identified in a typical BLAST search. These short sequences may be located by searches of motif databases.
■ A protein family comprises multiple proteins all derived from the same ancestral protein. The genes encoding these proteins, which constitute the corresponding gene family, arose by an initial gene duplication event and subsequent divergence during speciation (see Figure 9-32).
■ Related genes and their encoded proteins that derive from a gene duplication event are paralogous; those that derive from speciation are orthologous. Proteins that are orthologous usually have a similar function.
■ Open reading frames (ORFs) are regions of genomic DNA containing at least 100 codons located between a start codon and stop codon.
■ Computer search of the entire bacterial and yeast genomic sequences for open reading frames (ORFs) correctly identifies most protein-coding genes. Several types of additional data must be used to identify probable genes in the genomic sequences of humans and other higher eukaryotes because of the more complex gene structure in these organisms.
■ Analysis of the complete genome sequences for several different organisms indicates that biological complexity is not directly related to the number of protein-coding genes (see Figure 9-34).
■ DNA microarray analysis simultaneously detects the relative level of expression of thousands of genes in different types of cells or in the same cells under different conditions (see Figure 9-35).
■ Cluster analysis of the data from multiple microarray expression experiments can identify genes that are similarly regulated under various conditions. Such co-regulated genes commonly encode proteins that have biologically related functions.
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