Revision with unchanged content. Bioinformatics is a relatively new discipline within Biology that has contributed significantly to the development of biological knowledge. It uses a variety computational tools, such as BLAST and DNA microarrays, that have become almost ubiquitously used in the biological world. This work demonstrates that these tools utilize the scientific methods of extended cognition, analogical reasoning, and representations of mechanisms. This analysis of Bioinformatics and its tools and processes is the first comprehensive work of its kind. It is intended to present that Bioinformatics should not only be of interest to biologists, but also to philosophers on how Biology is radically changing through Bioinformatics. Also relevant is how various scientific methods, generally thought to be cursory to the scientific enterprise, actually take on a more central role.