An Introduction to Bioinformatics Algorithms - I - page1-78

6/24 give me example what is pseudocode; 6/25 biological algorithm is even more complicated than computer algorithm; how to solve change problem. 6/28. Use Fibonacci to illustrate the difference between Iteration and Recursion, iteration has a for i <- 1 to n-1, recursion repeats itself time to time. Iteration save more time. 6/29. illustrate the differences between exponential and polynomial algorithm. Big O notation, give the worst cast efficiency, it is upper bound. In contrary, f(n) = Ω(g(n)) indicate f(n) grows not slower than g, it is lower bound. 

7/05. Induce the Big O as an exponential and polynomial function for HANOITOWER and SORT problems. As for the algorithm design, it talks about several basic algorithms. Exhaustive algorithm (brute force)often takes a long time, and most of efforts in this book is to find an alternative instead of brute force; Branch and Bound algorithm (prune) moves out the branch unnecessarily to search; Greedy algorithm often choose the most attractive choice. In many cases, greedy algorithm seems to be obvious and natural, but will be subtle wrong; Dynamic programming breaks a large problem into small sub-problems, and try to organize computations to avoid recomputing values. But cannot figure out how does the “Rocks Game” can be related with dynamic programming. 

7/06. other basic algorithms: divide and conquer algorithm, machine learning, randomized algorithm. NP-complete problems lie between exponential problem and polynomial problem. No polynomial algorithm has yet been found, yet nobody can prove that polynomial solution is not exist. Like traveling salesman problem. 

7/07. basic findings in biology: 1. cells -> chromosomes and genes, Morgan use fly to locate genes. -> constitutes of DNA, structure of DNA, DNA is what makes genes -> RNA is the transmit between DNA and protein, how DNA to RNA, how RNA to protein, the genetic code. Interesting techniques used by biologists: 1). how did they copy and amplify DNA fragments? by PCA or cloning (insert the fragment into cloning vector which is originated from virus and bacterium, then lead the DNA cycle into bacterium to let it reproduce.) Human genome can be represented by a library of 30,000 clones. 2). cutting and pasting DNA through restriction enzyme, ligase. 3). measure DNA length through gel. 4). probing DNA by a probe (with a bulb) supplementary to the target sequence, that is how RNA array did. 

Around 0.1% (3 million) of the 3 billion bases are different between any two individual.