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Computational Biology -: Unix/Linux, Data Processing and Programming …
Edition 2nd ed. Physical description 1 online resource xxix, : illustrations some color. Online Available online.
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In a similar vein, the instructions for ClustalW include compilation using a makefile. This is a very useful concept to understand but, unfortunately, it is glossed over here. Finally, the reader is instructed to run ClustalW in a way that circumvents its inbuilt menu system and builds an alignment purely on default settings. This gives a somewhat misleading view of the capabilities of the program. Part 4 devotes 58 pages to the awk scripting language before moving on to perl for the remainder of the book. The author uses awk as an introductory programming language and illustrates a number of basic programming concepts such as reading input from different sources, variables and print statements.
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The later chapters on perl cherry-pick features not available within awk, such as hashes, scalar variables and complex string manipulations. The content of the book seems somewhat skewed. The author has made a brave decision to spend a large proportion of the book teaching the awk scripting language. This would seem to move in a different direction to the majority of newer practitioners, who encourage the jump to learning perl earlier without resorting to heavy use of awk.
The introduction specifically mentions the common problem of manipulating file formats required by different programs, but no section defines any of the commonly used biological file formats. This would make file conversions more straightforward and could be usefully located within the appendix.
It was encouraging to see a mention of the Bioperl extensions, however brief, although sections on cgi scripting and MySQL would also have been useful. Since the book encourages the user to attempt scripting and later programming tasks for themselves, it would be helpful to discuss the concept of layout and paths in more depth, perhaps as a specific chapter.
Saving programs in consistent places, using links and bin directories are all useful concepts that can stop a machine from becoming hopelessly disorganized.
An extension of the chapter, covering installation of third-party code, would also have been useful, even though a detailed discussion of make and debugging is outside the remit of this book. This topic is seldom seen in books and would empower the reader to attempt to install some of the many excellent Open Source programs available.
Inbuilt Unix and shell commands can handle a range of data processing tasks but many bioinformatics textbooks do not include them, and yet few people first venturing into computational biology from the bench would turn to a pure Unix textbook for ideas. Integration of genetic and epigenetic changes in cancer including mutations, gene expression data, epigenetic.
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