Chapter 1: Introduction -- Chapter 2: DNA sequence assembly and annotation of genes -- Chapter 3: Databases and protein structures -- Chapter 4: Pair-wise alignment, multiple alignment and BLAST -- Chapter 5: Primer design -- Chapter 6: Short introduction to phylogenetic analysis of molecular sequence data -- Chapter 7: Sequence based classification and identification of prokaryotes -- Chapter 8: 16S rRNAampliconsequencing for metagenomics -- Chapter 9: Full DNA metagenomics -- Chapter 10: Transcriptomics -- Chapter 11: Molecular typing of prokaryotes.

This textbook introduces to the basic concepts of bioinformatics and enhances students' skills in using software and tools relevant for investigations in microbiology. The most relevant methods to analyze data are shown and readers are introduced on how to draw valid conclusions based on the results obtained. Software and servers which are free to use on the internet are presented and more advanced stand-alone programs are suggested as a second option. Exercises and training quizzes are provided at the end of each chapter to facilitate learning. The book targets Ph. D. students and advanced undergraduates in microbiology, biotechnology, and (veterinary) medicine with little to basic knowledge in bioinformatics. .