By Paul G Higgs; et al
Preface.Chapter Plan.Chapter 1. advent: The Revolution in organic Information.Chapter 2. Nucleic Acids, Proteins, and Amino Acids.Chapter three. Molecular Evolution and inhabitants Genetics.Chapter four. types of series Evolution.Chapter five. info assets for Genes and Proteins.Chapter 6. series Alignment Algorithms.Chapter 7. looking series Databases.Chapter eight. Phylogenetic Methods.Chapter nine. styles in Protein Families.Chapter 10. Probabilistic equipment and computer Learning.Chapter eleven. additional issues in Molecular Evolution and Phylogenetics.Chapter 12. Genome Evolution.Chapter thirteen. DNA Microarrays and the 'omes.Mathematical Appendix.List of net address.Glossary.Index
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Extra resources for Bioinformatics and genome biology
Protein sequences are traditionally written from the N to the C terminus, which corresponds to the direction in which they are synthesized. The four atoms involved in the peptide bond lie in a plane and are not free to rotate with respect to one another. This is due to the electrons in the chemical bonds, which are partly delocalized. The flexibility of the protein backbone comes mostly from rotation about the two bonds on either side of each α carbon. Many proteins form globular three-dimensional structures due to this flexibility of the backbone.
This is known as splicing. Splicing is carried out by the spliceosome, a complex of several types of RNA and proteins bound together and acting as a molecular machine. The spliceosome is able to recognize signals in the premRNA sequence that tell it where the intron–exon boundaries are and hence which bits of the sequence to remove. As with promoter sequences, the signals for the splice sites are fairly short and somewhat variable, so that reliable identification of the intron–exon structure of a gene is a difficult problem in bioinformatics.
In the rest of the chapter, we want to introduce some simple methods for data analysis that are useful in bioinformatics. We will use the data on amino acid properties. 2 shows eight properties of each amino acid (and we could easily have included several more columns using data from additional sources). It would be useful to plot some kind of diagram that lets us visualize the information in this table. It is straightforward to take any two of the properties and use these as the coordinates for the points in a two-dimensional graph.
Bioinformatics and genome biology by Paul G Higgs; et al