The objective of this course is to introduce students to the main tools and algorithmic principles of DNA and protein sequence analysis. It introduces the main public databases accessible on-line and the interface to interrogate them.

It adresses the problems of sequence and genome reconstruction and content, the major tools for sequence comparison, sequence alignement and homology search.

It also adresses the topics of analysing and extracting biological information from sequences using computational tools, available either locally or on online servers and portals:

• Motifs, patterns, signals
• Content and statistical sequence analysis

It is not a programming course per se, but it provides students with the core understanding of major algorithms and computational principles involved, which should allow them to implement the corresponding code, should they need to. It also provides them with a critical view of the strength, scope and limits of currently available tools in the field of computational biology of sequences.

It also introduces some general principles and tools of computer science in the context of biological applications: Dynamic programming, regular expressions, finite-state automata, Markov models and hidden Markov Models.