This is the companion website for the book “Introductory Bioinformatics” by Stefanie Hartmann and Joachim Selbig. This site contains the following information:
  1. •About the book
  2. •Table of contents
  3. •Data files
  4. •Required software
  5. •Bootable linux OS with software and data files pre-installed
  6. •Contact information
  7. •Errata and updates
 
Abuout the book
Stefanie Hartmann and Joachim Selbig teach bioinformatics courses at the University of Potsdam. For their undergraduate course they wanted a textbook that introduced students to the field of bioinformatics, with a focus on the analysis of sequences and structures. Because they use the Linux operating system and the statistics software R for the computer exercises, they also wanted an introductory text on these topics. Since the authors couldn't find a book that contained the exact mix of things they are teaching in their course, they decided to write their own. This book also contains computer exercises, the data for which can be downloaded from this web-site.
 
Table of contents
I First things first: assembling your toolkit
   1. What is a gene?
   2. Protein structure
   3. Speedy and efficient data analysis
   4. The terminal is your friend
   5. /r[e-g]{2}ular expres+ions/
   6. R
II On your bioinformatics marks, ready – set – go!
   7. The information superhighway
   8. Pairwise sequence comparisons
   9. Multiple sequence alignments
  10. Trees
  11. Analysis and prediction of secondary structure
  12. Comparison of 3D structure
  13. Prediction of 3D structure
  14. Statistically describing and displaying bioinformatics data
 
 
Data files
Data files that are used for the computer exercises at the end of the chapters are available here. All data can be downloaded together, you can also download data for selected exercises only. Right-click on the the links below to download the files:
  1. •all data: data.zip  
  2. •Chapter 4:  CH4exercise.zip
  3. •Chapter 5: proteins.fasta, dna.fasta
  4. •Chapter 6: PDB_SS.txt
  5. •Chapter 7, 9, 11: globins.fasta
  6. •Chapter 8: medicago_pep.fasta.zip, medicago_dna.fasta.zip
  7. •Chapter 10: globins.aln
  8. •Chapter 14: GOR_data.R
 
Required software
  1. •Chapter 4, 5, and preferably all others: a Linux OS
  2. •Chapter 6, 14, 15: R
  3. •Chapter 7, 8, 11: internet browser of your choice
  4. •Chapter 8: BLAST, text editor of your choice
  5. •Chapter 9: ClustalW, ClustalX
  6. •Chapter 10: ClustalX, Phylip
  7. •Chapter 13: internet browser, text editor
 
 
Bootable linux OS with software and data files pre-installed
If your computer is running a WIndows OS, you can use the provided BioMasonux OS to complete all exercises of the book:
  1. •download the ISO-file provided here. (>500 MB!)
  2. •use the software of your choice (for example, the freely available ImgBurn) to burn this ISO-file onto a CD or DVD
  3. •set the boot order of your computer such that it starts from CD/DVD
  4. •insert the CD/DVD and start your computer; it will boot from the inserted CD/DVD
  5. •once the prompt “boot:”  appears, just hit the “Enter/Return” key
  6. •BioMasonux, a Ubuntu-based Linux with all the required data and software installed, will start from the CD/DVD
NOTE: do this at your own risk. We are not responsible for lost data, overwritten hard drives, or other damage.
 
 
Contact us
We worked hard on this book, but mistakes do happen. If you see a mistake or have other feedback for us, please send us an email at bioinf@senita.de. Errata and updates will be posted at this website.
 
Errata, first edition (August 2009): errataV1.pdf
 
Errata, second edition (October 2010)
  1. •the order of the clues for the crossword puzzle on p. 15 got a little mixed up. Here is the correct version: clues.pdf  
  2. •Ch 4, p. 52: the last sentence on p. 52 should read “The output of this command is therefore a single number: 5.”
 
 
 
Introductory Bioinformatics
 
companion website