shuron-index

FrontPage

案１ (2006/06/28)

• 河田さんの修士論文の section 構成を参考に、自分の研究を河田さんの section 構成に当てはめた感じ。

1. Introduction
2. Background
   1. Biological background on finding syntenies
   2. Local alignment algorithm
      1. abstruct of local alignment
      2. biological findings
      3. optimal local alianment algorithms
      4. Heuristic local alignment algorithms
      5. probabilistic interpretation
      6. score matrix
   3. Probabilistic model and parameter learning alrorithms
      1. Conditional, joint and marginal probabilities
      2. Bayes' theorem
      3. Probabilistic model
      4. Muximum Likelihood estimation
      5. Psudocount
      6. Muximum a posteriori estimation
      7. Weighted bayesian parameter estimation
      8. Expectation maximum method
3. Previous Works
   1. Works for detecting anchors
      1. BLAT
      2. Sim4
      3. PatternHunter?
      4. BLASTZ
      5. PipMaker?
      6. CHAOS
      7. murasaki
   2. Works for finding syntenies based on detected anchors
      1. GRIMM-Synteny
      2. LAGAN
      3. Mauve
4. Methods
   1. Local genome alignment and synteny finding
   2. Probabilistic model on local genome alignment
   3. Dynamic Programming for local genome alignment
   4. Learning algorithm for local genome alignement
   5. Summary of local genome alignemnt
5. Experimental Results
   1. Dot-plot view
   2. 尤度関数と収束パラメータの初期パラメタ依存性
   3. GO-term を用いた in-synteny genes の機能解析
6. Discussion
7. Conclusion
   1. Conclusion
   2. Future Direction

• Acknowledgement
• Reference