Bioinformatics/Sequence Data
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This section deals with the underlying properties of individual biological macromolecules, their structures, and corresponding digital representations.
Each chapter is organized around "wet-lab" experimental techniques used to obtain data of a certain sort, and in silico techniques used to support or enrich the experimental results.
This section concentrates heavily on introducing concepts in biology or biochemistry which are likely unfamiliar to those with a background in computer science or mathematics. Individuals with a strong background in biochemistry or molecular biology will probably want to skip this section entirely, or just skim over it to the computational sections, if they are unfamiliar.
In most cases, proteins and nucleic acids are treated together in each section.
Chapter one covers experimental techniques used to obtain primary sequence data - genomes, and the computational techniques used to treat that data.
The following sections from other wiki textbooks may be helpful as background:
Chapter two covers some of the biochemical and biophysical properties of biological macromolecules, and some of the language-like properties of biological macromolecules that make it productive to study digital representations of those macromolecules.
The following sections from other wiki textbooks may be helpful as background:
Chapter three covers the biophysical properties of biological polymers that cause them to fold reliably into specific secondary and tertiary structures, and experimental techniques used to determine those structures. Computational techniques to treat structural data are also introduced.
The following sections from other wiki textbooks may be helpful as background:
Chapter four discusses intermolecular recognition and quaternary structures. Experimental techniques to identify molecular interaction partners are discussed. Computational techniques to treat interaction data are introduced.
The following sections from other wiki textbooks may be helpful as background:
Chapter five introduces experimental techniques in enzymology and the biophysical basis of enzyme catalysis. It includes a review of some methods of function determination from sequence data.
The following sections from other wiki textbooks may be helpful as background:
Chapter six covers the so-called central dogma of molecular biology: DNA codes for RNA codes for protein. It covers some of the experimental techniques used to determine transcription and translation levels, and some of the computational techniques used to treat that data.
The following sections from other wiki textbooks may be helpful as background:
Chapter seven goes into more detail on sequence motiffs found in nucleic acids, and one how the structures of those motiffs alter the transcription of genes. Computational methods in transcriptional studies are discussed in more depth, and experimental techniques to obtain transcriptional information are covered in more detail.
The following sections from other wiki textbooks may be helpful as background:
Chapter eight - maybe I should delete this chapter it seems redundant with chapter five.
Chapter nine includes a summary of all computational techniques introduced in the first section, with discussion on how those techniques can be applied to make predictions based on a single sequence or structure.
--Samuel.handelman 21:47, 14 Oct 2004 (UTC)
