By Jonathan Pevsner
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Extra resources for Bioinformatics and Functional Genomics
Org/chapter5). The student thus chooses the name of the gene and its corresponding protein and describes information about the organism and evidence that the gene has not been described before. Then, the student creates a multiple sequence alignment of the new protein (or gene) and creates a phylogenetic tree showing its relation to other known sequences. Each year, some beginning students are slightly apprehensive about accomplishing this exercise, but in the end all of them succeed. A benefit of this exercise is that it requires a student to actively use the principles of bioinformatics.
For additional definitions of bioinformatics and functional genomics, see Boguski (1994), Luscombe et al. (2001), Ideker et al. (2001), and Goodman (2002). Bioinformatics and Functional Genomics, Second Edition. By Jonathan Pevsner Copyright # 2009 John Wiley & Sons, Inc. 3 4 INTRODUCTION protein. Functional genomics describes the use of genomewide assays in the study of gene and protein function. The aim of this book is to explain both the theory and practice of bioinformatics and genomics. The book is especially designed to help the biology student use computer programs and databases to solve biological problems related to proteins, genes, and genomes.
The three interior circles show the reconstructed ancestral sequences obtained by combining the paired sequences from each previous step. The inner circles are progressively smaller and reﬂect fewer conserved genes with a smaller average similarity. From Aury et al. (2006). Used with permission. 18. Alignment of C. elegans and C. org). Regions of chromosome I are aligned from C. elegans (above) and C. briggsae (below). PartI Analyzing DNA, RNA, and Protein Sequences in Databases The study of bioinformatics includes the analysis of proteins.