BOOK

This is the companion website for the book “Introductory Bioinformatics” by Stefanie Hartmann and Joachim Selbig. The fourth edition from March 2013 is the most recent one; it is available in print format and as an eBook.


Abuout the book

Together with Joachim Selbig I teach the undergraduate bioinformatics course at the University of Potsdam. We wanted a textbook that introduced students to the field of bioinformatics, with a focus on the analysis of sequences and structures. Because for the computer exercises in our course we use the Linux operating system and the statistics software R, we also wanted an introductory text on these topics. Since we couldn't find a book that contained the exact mix of things we are teaching in our course, we decided to write our own. We included 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:
•all data: data.zip
•Chapter 4: CH4exercise.zip
•Chapter 5: proteins.fasta, dna.fasta
•Chapter 6: PDB_SS.txt
•Chapter 7, 9, 11: globins.fasta
•Chapter 8: medicago_pep.fasta.zip, medicago_dna.fasta.zip
•Chapter 10: globins.aln
•Chapter 14: GOR_data.R


Required software

•Chapter 4, 5, and preferably all others: a Linux OS
•Chapter 6, 14, 15: R
•Chapter 7, 8, 11: internet browser of your choice
•Chapter 8: BLAST, text editor of your choice
•Chapter 9: ClustalW, ClustalX
•Chapter 10: ClustalX, Phylip
•Chapter 13:
internet browser,text editor


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.



Stefanie Hartmann 2013