1.3: Additional materials

Online Materials for Fall 2015

lecture1_transcript.html#Handouts

In addition to these static notes, the course has several online resources:
• The course calendar on Google Calendar. You can add ”6.047 Lectures”, a public calendar. • The NB note-taking system for annotating these notes http://nb.mit.edu/

Textbooks

lecture1_transcript.html#CourseInformation The following three (optional) reference textbooks are recommended for the class.

1. Richard Durbin, Sean R. Eddy, Anders Krogh and Graeme Mitchison, Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids.
2. Neil Jones and Pavel Pevzner, An Introduction to Bioinformatics Algorithms.
3. Richard Duda, Peter Hart, David Stork, Pattern Classification.

Each book has a different advantage. The first book is a classic one. It is heavy in math and covers much of what is in class. The book is focused on sequence alignment. As part of sequence alignment theory, the book approaches Hidden Markov Models (HMM), pairwise and multiple alignment methods, phylogenetic trees as well as a short background in probability theory.

The second book intends to balance between mathematical rigor and biological relevance. According to the author, it is a good book for undergrad students. The book includes a table that associates algorithms to biological problems.

The third book is about machine learning. It takes more of an engineering approach. It includes machine learning theory, neural network and, as the name suggests, pattern recognition.