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Genomics and Bioinformatics [Kindle Edition]

Tore Samuelsson
3.0 out of 5 stars  See all reviews (2 customer reviews)

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Book Description

With the arrival of genomics and genome sequencing projects, biology has been transformed into an incredibly data-rich science. The vast amount of information generated has made computational analysis critical and has increased demand for skilled bioinformaticians. Designed for biologists without previous programming experience, this textbook provides a hands-on introduction to Unix, Perl and other tools used in sequence bioinformatics. Relevant biological topics are used throughout the book and are combined with practical bioinformatics examples, leading students through the process from biological problem to computational solution. All of the Perl scripts, sequence and database files used in the book are available for download at the accompanying website, allowing the reader to easily follow each example using their own computer. Programming examples are kept at an introductory level, avoiding complex mathematics that students often find daunting. The book demonstrates that even simple programs can provide powerful solutions to many complex bioinformatics problems.


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Review

'The book provides a lively and accessible introduction to current research in the life sciences, and it does so in a succinct way by grounding the explanations with simple algorithms expressed in Perl code. As such, the book can be very useful to a general science audience, particularly those with a computer science background, whether established researchers or undergraduate students. The writing is inspiring and engaging, and the inclusion of Perl code makes it easy for readers to apply the knowledge and observe the outcomes.' Sara Kalvala, Computing Reviews

Book Description

Designed for biologists without programming experience, this textbook provides a hands-on introduction to Unix and Perl tools for bioinformatics. Relevant biological examples are combined with practical computational procedures, teaching students how to proceed from biological problem to bioinformatics solution. An accompanying website provides files, scripts and solutions to end-of-chapter exercises.

Product details

  • Format: Kindle Edition
  • File Size: 4298 KB
  • Print Length: 358 pages
  • Simultaneous Device Usage: Up to 4 simultaneous devices, per publisher limits
  • Publisher: Cambridge University Press; 1 edition (28 Mar. 2013)
  • Sold by: Amazon Media EU S.à r.l.
  • Language: English
  • ASIN: B009ZRNOKW
  • Text-to-Speech: Enabled
  • X-Ray:
  • Word Wise: Not Enabled
  • Average Customer Review: 3.0 out of 5 stars  See all reviews (2 customer reviews)
  • Amazon Bestsellers Rank: #846,267 Paid in Kindle Store (See Top 100 Paid in Kindle Store)
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More About the Author

After having studied math and chemistry I started out my scientific career as an experimental biochemist. With "experimental" I mean in this case "wetlab" as opposed to the in silico world. For about twenty years I actually did quite a lot of pipetting, mixing, fractionation, purification, and what have you, in order to address different biochemical problems. This was in fact partly in the experimentally difficult days of B.C. ("Before Cloning"). As a consequence a biochemist would at the time often carry out very cumbersome protein purification, starting out with tons of biological raw material and ending up, hopefully, with a few milligrams of reasonably purified protein. Having said this you have come to realize that I'm not too young.

In addition, no one knew about computers in those days. However, I must have had an interest in computational matters because I remember that early during one of my university math courses there was an element of programming and I found that really interesting. The language was called ALGOL, not so popular today. One significant problem at the time was that once having written some code, there was no computer around for trying it out. It was simply a matter of writing pieces of code on a piece of paper. There must have been computers around somewhere but I guess only senior scientific staff had access to those.

Then came the days of cloning and gene technology and I became very interested in analysis of DNA and protein sequences. One commonly used software for sequence analysis in the 80s and 90s was the Genetics Computer Group (GCG) software suite, in our case running on a VAX computer system, and I used in extensively. One research project of mine was to clone and sequence tRNA genes. I had no access to software that could identify these genes and print their secondary structure. As I was interested in programming I therefore wrote some code in PASCAL to do that. And looking at the code now, it was rather awful, as I had no previous experience of programming.

Eventually I got so much involved in biological sequence analysis that I became a full time bioinformatician. In the early 1990s I started to learn about Unix and Perl. In 2001 an international master's program in bioinformatics was initiated at the Chalmers University of Technology in Gothenburg, Sweden; at that time the first programme of this kind in the country. I was for many years a teacher in that bioinformatics program. I was fortunate to meet a large number of highly motivated international students in that programme and I noted in particular that students had widely different educational backgrounds and I noted the very wide spectrum of disciplines from where bioinformaticians are recruited.

Quite recently high-throughput sequencing has revolutionized biology and has caused a renewed interest in biological sequence analysis. I started to write on the book "Genomics and bioinformatics ..." in April 2010. One major idea I had was that I should present a number of rather specific biological problems and how these may be addressed using relatively simple Unix and Perl tools. Hence, the reader would be attracted by the biological problem posed and eager to know about the computational stuff needed to tackle it. I also wanted a design with all practical details of the bioinformatics so that a student could follow all the way from problem to final solution. For this reason all material referred to in the book is available from a web supplement (http://bio.biomedicine.gu.se/gb/). A typical reader of this book would be a life scientist with no previous background in computational techniques such as Unix and Perl but with an interest to learn more about these things. I also wanted the biology parts to be fairly well-explained so that even a student without much molecular biology background would be able to understand what kind of problems are examined in genomics and bioinformatics.

A large number of people were supportive during the writing, including staff at the Cambridge University Press. Writing a textbook always takes more time than you initially think but by and large, I really enjoyed writing this book!

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Most Helpful Customer Reviews
2 of 2 people found the following review helpful
5.0 out of 5 stars Excellent and up-to-date review of genomics 26 Jan. 2013
Format:Kindle Edition|Verified Purchase
As someone with a foot in both worlds (biology and programming) I found this book extremely helpful when starting in a new field of research (genomics). The topics covered here are interesting and relevant, and the literature cited is very current, making this book ideal for anyone starting study in this field. I also thought the approach to introducing Perl programming was excellent (by teaching it from an applied route). I do not understand why the previous post only gave this book one star. I have already recommended this book to my student.
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0 of 9 people found the following review helpful
1.0 out of 5 stars GENOMICS AND BIOINFORMATICS 3 Oct. 2012
Format:Paperback|Verified Purchase
Interesting subject, modern science and technological change covered in detail, cheap pricxe, prompt delivery. Covers the use of the internet by and it's relevance to, scientific progress.
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Amazon.com: 3.7 out of 5 stars  3 reviews
2 of 2 people found the following review helpful
2.0 out of 5 stars Okay, but directionless 16 May 2014
By Alex Hall - Published on Amazon.com
Format:Kindle Edition|Verified Purchase
I used this book in an introductory grad-level bioinformatics course. No programming knowledge was necessary to enroll and we learned python as part of this course. This book was required, but I only used it for the first week or two of class. Really not that helpful for my needs.

My main issue with the book is the general lack of editorial feel. Most chapters are topical case studies which also describe how to do a task in perl (there is a companion website which provides equivalent python scripts). Especially since we were learning Python in this course and considering that the field is moving towards object-oriented languages, I rarely needed to reference this book.

There are several better introductions to genomics, so if you aren't interested in the 'how-to' of this field then I recommend passing on this book. Even if you are interested, consider other resources before this one.
2 of 2 people found the following review helpful
5.0 out of 5 stars Nice update for any scientist who needs to review the new genomics tools 20 July 2013
By Piotr Krasucki - Published on Amazon.com
Format:Paperback|Verified Purchase
Use this a a desk reference to leverage new genomics tools. Relatively well written summary - starting point. Strongly recommended
4.0 out of 5 stars Informative 8 July 2014
By NH - Published on Amazon.com
Format:Kindle Edition|Verified Purchase
This is a useful and informative text; although I won't be using it "extensively" until next semester, I have scanned the chapters and it appears to have the right content for studying the subject thoroughly. I look forward to supplementing class lectures with the info contained in this text.
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