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Our bodies are extraordinary machines: exible in function, adaptive to new environments, and able to interact and reproduce All these capabilities are speci ed by a program unique to each of us, a string that is 3 billion characters long over the alphabet {A, C, G, T } our DNA The DNA sequences of any two people differ by only about 01% However, this still leaves 3 million positions on which they vary, more than enough to explain the vast range of human diversity These differences are of great scienti c and medical interest for instance, they might help predict which people are prone to certain diseases DNA is a vast and seemingly inscrutable program, but it can be broken down into smaller units that are more speci c in their role, rather like subroutines These are called genes.

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Computers have become a crucial tool in understanding the genes of humans and other organisms, to the extent that computational genomics is now a eld in its own right Here are examples of typical questions that arise 1 When a new gene is discovered, one way to gain insight into its function is to nd known genes that match it closely This is particularly helpful in transferring knowledge from well-studied species, such as mice, to human beings A basic primitive in this search problem is to de ne an ef ciently computable notion of when two strings approximately match The biology suggests a generalization of edit distance, and dynamic programming can be used to compute it Then there s the problem of searching through the vast thicket of known genes: the database GenBank already has a total length of over 10 10 , and this number is growing rapidly.

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The current method of choice is BLAST, a clever combination of algorithmic tricks and biological intuitions that has made it the most widely used software in computational biology 2 Methods for sequencing DNA (that is, determining the string of characters that constitute it) typically only nd fragments of 500 700 characters Billions of these randomly scattered fragments can be generated, but how can they be assembled into a coherent DNA sequence For one thing, the position of any one fragment in the nal sequence is unknown and must be inferred by piecing together overlapping fragments A showpiece of these efforts is the draft of human DNA completed in 2001 by two groups simultaneously: the publicly funded Human Genome Consortium and the private Celera Genomics 3.

8. Select whether to print a test page or not, then click Finish. Windows will load the printer s driver or ask you to supply a third-party driver. The default printer is the one to which all print jobs will be sent unless you specify otherwise in the application from which you are printing. When the printer is successfully installed, the Printers window will be displayed with an icon representing all printers in the system (including the new one). The default printer might be indicated by a check mark. To configure a printer as the default, right-click its icon, then select Set as Default. You can configure a printer s settings by accessing its properties. Right-click the appropriate printer s icon and select Properties. A window similar to Figure 9-27 will open. Note that this window is the Printer Properties window on a Windows XP system. Depending on the manufacturer s design, you might be able to use this window to set the resolution, paper type, color use, and density of the printer. Many printers also include test and cleaning modes in this window.

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When a particular gene has been sequenced in each of several species, can this information be used to reconstruct the evolutionary history of these species We will explore these problems in the exercises at the end of this chapter Dynamic programming has turned out to be an invaluable tool for some of them and for computational biology in general..

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