Chemical Genomics

The book’s first few chapters deal with an introduction to bioinformatics, sequence analysis, and the diverse Internet resources currently available. The following chapters guide the reader through the databases of BLAST: BLASTN, BLASTP, BLASTX, and TBLASTN. Each chapter is set up to conduct you through a particular example query (or two), and is supplemented with specific screen shots from the database so that it is possible to follow along, whether you are on your computer doing the search in conjunction with the author or not. This was extremely valuable. The author then describes thoroughly how results could be interpreted and the different parameters that could be changed depending on your query, as well as other databases available that may be more useful depending on the sequence you are working with. The following chapters include tutorials on how to use websites such as NEBCutter, Primer3, Sequence Retrieval System (SRS), and DotPlot as general lab utilities, PROSITE for protein analysis, Transfac for discovering transcription factor binding sites, miRBase, KEGG, and TargetScan to navigate the structures, locations, and functions of miRNAs, and the UCSC Genome Browser. The conclusion of each chapter presents a series of exercise questions that are useful tools to perform additional searches and further explore the capabilities of the bioinformatics databases available. This textbook would be useful to any biologist, as its chapters span RNA sequencing to protein analysis to miRNA target prediction. It is hard to think of a database currently available online on which this text does not include a detailed tutorial. It would serve as a great reference for starting a sequencing analysis, troubleshooting a difficult sequence, or discovering more about an interesting sequence. As someone who is unfamiliar with many of the finer details of sequencing analysis, I found this text easy to read and understand, and it made bioinformatics appealing to learn about, as some pages contained highlighted boxes of interesting facts about the history of sequencing, biology, or various discoveries. I appreciated that the book took the time to explain how the databases worked, so that you could better understand their capabilities, instead of just telling you what to enter in each field on each query screen. The potential for such online databases is immense and will only continue to grow in the future as more data is amassed and compiled on the Internet. Such textbooks such as Practical Bioinformatics will be invaluable to the general researcher or student, if only as a starting point for the databases to come.