Bioinformatics and Functional Genomics 3rd Edition

Part II: Functional Genomics: Bioinformatics from DNA to RNA to Protein

The central dogma of molecular biology states that DNA is transcribed into RNA and may be further translated into protein. In bioinformatics and genomics we extend this to say that the collection of DNA (the genome) may be transcribed to the collection of all RNAs (the transcriptome) which may be translated into a collection of proteins (the proteome).

In the middle section of the book we follow this flow. Chapter 8 introduces the chromosome (including topics such as the ENCODE Project, definitions of repetitive DNA and of genes, and measurement of variation in DNA). Chapter 9 introduces next-generation sequencing including many software tools used on the Linux operating system. Chapter 10 introduces ribonucleic acid (RNA) from a bioinformatics perspective, while Chapter 11 explains both microarrays and RNA-seq to measure RNA transcripts. Chapter 12 is on proteomics, discussing mass spectrometry and X-ray crystallography, and considering four perspectives (protein physical properties; families; location; and function). Chapter 13 discusses protein structure. We end this section with a chapter on functional genomics, defining this field of study and discussing a variety of approaches.