Welcome to CS795/BINF 730 Biological Sequence Analysis.

Announcements

• 05.07.2009: All projects have been graded. Have a wonderful summer. Feel free to stop-by and pickup your final reports. Here is a distribution of the grades:
  
• 05.01.2009: 6 out of 17 voted for Meghana as the top choice for presentation. She is awarded extra credit.
• 04.30.2009: The grading scheme is 20% for A3, 20% for MT, 15% for A1, 15% for A2. Here is a distribution of your scores without the projects (out of 70).
  
• 04.29.2009: The last class will be held on Friday May 1, 2009 in room #4201 of the new engineering building or academic VI. See map with the building highlighted
• 04.29.2009: Excellent work class. Good round of presentations. C. Miles and J. Kauffman for Path to Network Alignment get 10 votes out 18 and are winners for the extra credit.
• 04.21.2009: Here is the schedule we will follow for the classroom presentations. Each group will be allowed 15 minutes of presentation only. I had like to emphasize this, since we are a lot of projects. There are penalty points for going overboard. Ideally you should plan for 12 minutes of presentation and 3minutes for questions. Also mail me your slides in "pdf" a night before your presentation day. We will be using my laptop only. Thanks.
  Day 1, 04.29.2009 ( in krug hall 5)
  1. Sean Smith
  2. Seogwon Kim
  3. Nipun Kakkar and Ronak Shah
  4. Shilpa Katta & Saranya Padmanabhan
  5. Sudheendra Bhat
     Samuel Suhas Singapogu
  6. D. Boddepalli, A. Nuhanovic
  7. C. Miles, J. Kaufman-Osborn
  8. Neerja Katiyar and Hoang
  9. Jeffrey Hoel

  Day 2, 05.01.2009

  1. Shanmuga Reddy Chitipiralla, Rithika Ganni
  2. Chris Parson
  3. MEGHANA VEMULAPALLI
  4. Sravanthi Joginipelli and Dinesh Jamjam.
  5. Michael Paton
  6. David Bagheri
  7. Ammar Naqvi
  8. Yumn Abduljawad
• 04.21.2009: My new office is 4423 in the Engineering Building. S. Kim has been awarded an extra 5 points for the best performing secondary structure prediction algorithm.
• 04.16.2009: The department is MOVING . It might be hard to find me for the next few days.
• 04.15.2009: Project Details (Reporting and Grading Scheme Updated). See Projects Page
• 04.09.2009: The TA, Rashmi will no longer be holding office hours. If you need to see her schedule an appointment by emailing her.
• 04.09.2009: There will be no class on 04/22/2009. We will have the presentations on two days: 04/29/2009 and 05/01/2009 both from 4:30 - 7:10 pm. The reports will be due on 05/06/2009 by email (pdfs only). Please go to the class forum and sign up
• 04.09.2009: Today's class we talked about massive genome sequencing. Check this link from BBC.
• 04.02.2009: Follow up classes that could be taken in Fall 2009:- (i) CS 795 (Biological Data Mining) or (ii) CS 795 (Geometrical Methods for Physical and Biological Computing) Both these classes are cross-listed with BINF.
• 03.25.2009: Important Message: The class projects are not due until May 6, 2009 (mid-night). During your presentations it is ok not to have some of the results that will go into your final report. Also please do literature search to know which other kinds of methods exist that attempt to solve the problem you proposed. I like most of the projects and will have feedback soon.
• 03.19.2009: Regarding A2. I tried entering the tree in the MLAGAN and it works fine. Only thing is that the naming convention that it follows. It takes as default the sequence names to be sequence1, sequence2, etc hence your tree should potentially look like ((sequence1 sequence2) sequence3) instead of the original sequence names.
• 03.16.2009: Schedule for the next few weeks
  

  03/18	Hidden Markov Models
  03/18	Intro. to Protein Structure Prediction
  03/25	Protein Structure Prediction
  04/01	Gene Prediction
  04/08	Sequence Assembly
  04/15	Metagenomics+ Transmembrane Proteins
  04/22+29	Project Presentations
  05/06	Project Report Due

• 03.16.2009: Excellent Resource Link. for sequence alignment.
• 03.03.2009: Extending deadline for project proposals to 03.25.2009. I am also posting several project suggestions in the "Projects" area. Here is a template from my last class in regards to what I expect in the project proposal.
• 03.02.2009: Assignment 3 is up.
• 03.01.2009: Assignment 2 is up.
• 02.25.2009: Please note the change in Syllabus. There will be no Mid-Term 2; just an additional Assignment.
• 02.23.2009: Solutions to HW1 posted in the Assignments Section.
• 02.18.2009: Results of the poll regarding pace of the class and assignment 1. Also the most frequent question was "do lsa by hand".
  
• 02.18.2009: To maintain fairness in class, no extensions for assignments. Assignment 1 is due on 02.18.2009. Please submit whatever you have. Explain what you have managed. Only single groups get an extension with a 10% penalty till Saturday.
• 02.16.09: Syllabus for mid-term includes chapters on introduction, pairwise alignment, scoring matrices, and multiple sequence alignment. Refer to the readings section and follow the topics of interest from there. The exam will be closed book, closed notes for about an hour + half.
• 02.16.09: Sample Mid-Terms: Paper1 and Paper 2
• 02.03.2009: Reading Section and Slides Updated at 3 pm EST
• 01.28.2009: TA information is updated.
• 01.28.2009: Assignment 1 is up. Its due on 02.18.2009 before class. It consists of a programming part and a written part. Have fun!
• 01.23.2009: Look at the forum for an interesting talk at NIH on personalized medicine.
• 01.21.2009: The next series of chapters that will be covered include chapters 4 and 5.
• 01.21.2009: I changed the Assignment 1 due date from 02.11.2009 to 02.18.2009.
• 01.19.2009: Please get accounts on this web-site for accessing secured content, forums, and other stuff.
• 01.17.2009: Class Website and Syllabus is Up! Have a great semester ahead. This is where all the news items would go. Keep track of this page.