In the past few years Next Generation Sequencing technologies have generated a huge amount of data at a very high pace. With thousands of fully sequenced genomes available, there is a compelling need for efficient algorithms to extract meaningful information from these data. In this talk I will present my research in the field of algorithms for bioinformatics analysis, with focus on efficient pattern discovery techniques. In particular, compact approaches and alignment free techniques will be discussed. Compact approaches perform a partition of the search space in classes to speed up computation, and reduce the size of the output. Alignment free techniques use the substring composition to compute similarity between sequences. These techniques are the solution of choice for genomes full comparison, where alignment-based techniques are very slow.