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Chapter 1Finding Out What BioinformaticsCan Do for YouIn This Chapter Defining bioinformatics Understanding the links between modern biology, genomi

After the nucleotides are linked, the resulting DNA strand exhibits an unusedphosphoryl group (PO4) at the 5' end, and an unused hydroxyl group (

By complementarity, we mean that a thymine (T) on one strand is alwaysfacing an adenine (A) (and vice versa) — and guanine (G) is always facing acytos

sequences. For instance, when living organisms reproduce, each of theirgenes must be duplicated. In order to do this, nature doesn’t go about it thewa

Such sequences are called palindromes, after the term for a phrase or sen-tence that reads the same in both directions (such as “Madam, I’m Adam” or“A

Table 1-2 (continued)1-Letter Code Nucleotide Base Name Category R A or G PurineY C or U Pyrimidine-- ------- None (gap)Some programs automatically ha

the basic elements of RNA secondary structure; they’re made up of loops (theunpaired C-U in Figure 1-8) and stems (the paired regions).Just for fun, v

the sequence of a protein is much more difficult than sequencing DNA — but all the proteins that a given organism (whether microbe or human being)can

origin of most of the so-called protein sequences that you can find in data-bases. Many sequence analysis programs acknowledge this fact by offeringon

Because of the triplet-based genetic code, a given DNA interval, on a givenstrand,can theoretically be translated in three different ways — basically

sequencing technologies improved steadily, but such technologies stilltended to concentrate on mining individual genes for information. During thisper

Time for a little bit of history. Before the era of bioinformatics, only two ways of performing biological experiments were available: within a living

Genome bioinformatics covered in this bookThe following list lets you know where in this book you’ll find more in-depthcoverage of specific topics (so

The early days of biochemistry were devoted to finding out a better way to represent proteins — preferably in terms of a formula that would explainthe

Biochemists then recognized that a given type of protein (such as insulin ormyoglobin) always contains precisely the same number of total amino acids(

Reading protein sequences from N to CThe twenty amino-acid molecules found in proteins have different bodies(their characteristic residues, listed in

The protein molecule itself is made when a free NH2group links chemicallywith a COOH group, forming the peptide bond CO-NH. Figure 1-2 shows aschemati

gives the protein its biological properties (for instance, its ability to digestsugar or to become part of a muscle fiber); those come from the three-

Protein bioinformatics covered in this bookThe study of protein sequences can get pretty complicated — so compli-cated, in fact, that it would take a

 Finding all proteins that share a similar sequence (Chapter 7) Classifying proteins into families (Chapters 7, 8, and 9) Finding the best alignmen