Bioengineering 240: Topics in computational biology and evolution

Spring 2007

Professor Kimmen Sjölander

Overview: This 3-unit class is aimed at graduate students from both the life sciences and engineering/maths. In addition to learning about bioinformatics methods in computational biology and evolution, we will focus on research and (oral and written) presentation skills, and on the development of critical and analytical skills. Readings for the class will be selected from the best papers in the field over the past 20 years, with a focus on review papers, and papers presenting important methods.

Prerequisite: Graduate standing, or consent of instructor.

Grading: Students will be graded based on two tasks: an original research project (80%, divided between written and oral presentations and a poster), a critical review of a published paper (10%), and reviews of other student research papers (10%).

  • Course calendar and grading details.
  • Frequently Asked Questions (FAQ) about the class.
  • Meeting schedule, for one-on-one meetings with students.

    How-to guides

  • Frequently asked questions about bioinformatics tasks.
  • Useful guides to using different software tools and web resources. See especially the contributed units to Current Protocols at the bottom of the page, and Lab Guide #1 (how to use Unix).
  • Using SAM software to reformat alignments for Belvu. This little guide tells you how to use the w0.5 software to construct an HMM, hmmscore to retrieve and align sequences to the HMM, uniqueseq to make the alignment non-redundant, and prettyalign to reformat the uniqueseq output so that you can view and edit the alignment using belvu.
  • Getting started on your project. These guidelines to using web resources to gather homologs, and the use of the SAM and HMMER HMM software tools for building HMMs and scoring sequence databases for remote homolog detection, will get you started on your projects.
  • A list of great webservers for protein structure and function prediction, including cellular localization.
  • Jake Gunn Glanville's handy toolkit.

    Lectures

  • Protein structure prediction: 2D and 3D structure prediction, Comparative model construction.
  • Multiple sequence alignment: part 1, part 2, part 3.

    Announcements
  • 2/2/06. Yahoo group for this course is at http://groups.yahoo.com/group/bioe240.
  • DECF computer accounts will be ready. Please go to 1109 Etcheverry during staff hours.

    Student papers

    will be available here. Please send your vote for best to Dan Kirshner. Be sure to mention the authors and title.


    Professor Kimmen Sjolander. email
    Berkeley Phylogenomics Group.