BIO/CSC295 2009F, Class 19: Structure Prediction (2)

Admin:
* Pop-Tarts!
* Don't forget the Medical Informatics talk at 4:30 today in 3821.  
  Refreshments at 4:15 in the CS Lounge.
* Don't forget the Destination ImagiNation Fun Run/Walk this weekend!
* Look ahead to the Rights and the Environment symposium next week.
* Today's programming project will be your next homework assignment.
  + Due Thursday
* We anticipate returning your exams some Tuesday.  
  + Sorry for the delay.
* Next reading from the literature: Krings et al. 1997.  
  + It's on P'Web.
  + Read and respond for Tuesday.
* Singers, 4:30 p.m. Sunday, S-L hall

Overview:
* Discussion: Picking independent projects.
  * About the projects
  * Ideas
  * Timetable
  * Form of the proposal
* Programming project: 7.5: Chou-Fasman.

About the projects
* Groups of three-four students
  + At least one biologist (or biochemist)
  + At least one non-biologist
* Pick an interesting problem in bioinformatics to work on
  + Requires biological data [probably from NCBI]
  + Requires computation
    - Can use a pre-built computational tool
    - Must use some tool you build yourselves WRITE CODE!
  + Use tool to do some analysi
  + Requires writeup
    - What was your hypothesis
    - What did the tool help you learn
    - Etc.
  + Requires a proposal

Questions
* Do we have to use existing algorithms?
  + You may use algorithms we've implemented already
  + You may use known algorithms that need to be implemented
    + A variant of the Kellis algorithm on a set of data you find
  + You may extend/change one of the algorithms we've implemented
  + You may create your own algorithm
    + Gene finder: Pick a set of similar genes.  Analyze the prefixes and
      suffixes of those genes for common paterns.  Write an algorithm that
      looks for those suffixes and prefixes to find genes

Project Timetable
* Thursday, 12 November: Turn in project proposals
* Tuesday, 17 November: Turn in peer reviews of project proposals
* Thursday, 19 November: Short (five minute) overviews of propoals for visitor
* Tuesday, 24 November, Status reports; In-class time for working on projects
* Thursday, 26 November, Thanksgiving
* Tuesday, 1 December, Status reports; In-class time for working on projects 
* Thursday, 3 December, PRESENTATIONS 
* Tuesday, 8 December, PAPERS + Code
* Thursday, 10 December, Wrapup

Vida says "Get together and talk about cool ideas."
* Look at some of the followup projects from the book that we didn't do!

Project 7-5: Chou-Fasman
* Find secondary struture in proteins
  + Alpha helices
  + Beta strands / sheets
  + Hairpin turns
* Statistical approach
  + "We've looked at lots of known protein structure and identified
     probability of each AA appearing in each structure"
  + For a new protein, we find sequences of high probability

Your goal(s)
* Implement the algorithm
  + Some infrastructure built already
* Test it carefully
 find 3 proteins and test your algorithm
 How many did it predict? How many were actually a-helix?
 How many did it miss?
 Did it find the entire helix (or predict one too long)?
 Improvements - find 3 and describe them.
 How do you find the improvements?  Literature search!

 Link to code in today's outline...