Homework of STAT 598K

1. Due on Wednesday, 9/5/01
   The first reference book "Biological sequence analysis", Ch2.4, 2.8, 2.9.
   
2. Due on Friday, 9/14/01
   The first reference book, Ch3.4, 3.5, 3.6 and
   Extra problem: Rewrite the Viterbi algorithm using the logarithm of all probablities.
   
3. Due on Friday, 9/28/01
   1). Why do we introduce position sensitive score system when aligning a sequence to a family? What are the similarities and differences of pairwise alignments and the alignment of a sequence to a profile?
   2). Derive a profile HMM from the multiple alignment in Figure 5.3.
   3). What are the relationships and differences of non-probabilistic methods and probability methods for sequence alignments? You can compare dynamic programming and HMM as a special example.

   The previous assignments are counted for 10% of the total grades.

4. The first written project is due on Friday, 10/12/01   (20% of the total grades).
   Some possible project topics

5. Class presentation assignments   (20% of the total grades).
   • 10/24, 10/26, Wenxuan Zhong and Hongmei Jiang,
     Block motif model for aligning local functional segments of proteins.
   • 10/31, 11/2, Chenghong Li, Yang Tian, and Jack Yang,
     Algorithms of predicting protein functions.
   • 11/7, 11/9, Chun Han and Yong Qiu,
     cDNA microarrays and oligonucleotide arrays.
   • 11/14, 11/16, John Stevens and Chuancai Wang,
     Cluster analysis of array data.
   • 11/28, 11/30, Nak-kyeong Kim and Junyong Park,
     Dimension reduction for array data.

6. The final exam includes a take-home exam and a written project. Both are due on 12/14, Friday.
   • The take-home exam will be available on 12/3, counted for 20% of the final grades.
   • The written project's topic will be chosen by student him/herself. Please begin the project early. It is counted for 30% of the grades. Please use 1.5 space. And the length should be over 5 pages, but less than 15 pages depending on the topic. Examples will be highly recommended in the final project.