This is a note for the book Genome-Scale Algorithm Design: Biological Sequence Analysis in the Era of High-Throughput Sequencing (2nd edition). Exercise 2.1 Consider the fail(·) function of the Morris–Pratt (MP) algorithm. We should devise a linear-time algorithm to compute it on the pattern to conclude the linear-time exact pattern matching algorithm. Show that one can modify […]
This is a note for the book Genome-Scale Algorithm Design: Biological Sequence Analysis in the Era of High-Throughput Sequencing (2nd edition). Exercise 1.3 In a given organism, some codons pairs occur less frequently than others. (a) Given the set of all exons of an organism, write a program that computes the ratio z(XY) between the observed and
This is a note for the book Genome-Scale Algorithm Design: Biological Sequence Analysis in the Era of High-Throughput Sequencing (2nd edition). Exercise 1.2 In a given organism some codons are used more frequently than others to encode the same amino acid. Given the observed frequency of every codon in a species, normalize it into probabilities and
This is a note for the book Population Genetics: A Concise Guide (Second Edition). Page 25 Problem 2.3 Convince yourself that the average time for the population to become homozyggous is , in fact, two generations. Note: The model is discussed here is a single hermaphroditic A1A2 heterozygote individual, wich means: (1) the population is
This is a note for the book Genome-Scale Algorithm Design: Biological Sequence Analysis in the Era of High-Throughput Sequencing. Exercise 1.1 Write a program that lists all the DNA sequences that encode a given protein sequence. From the wikipedia page DNA and RNA codon tables I got the inverse table for the standard genetic code
Page 24 Problem 2.2 If you know how to program a computer, write a simulation of genetic drift. Note: The simulation model: 1. Choose an allele at random from among the 2N (N is the number of the diploid individuals) alleles in the parent generation. 2. Make an exact copy of the allele. 3. Place
Page 14 Problem 1.3 Hardy-Weinberg frequencies in dioecious species may be investigated in an entirely different way. Let the genotype frequencies in females be x11, x12, and x22, and in males, y11, y12, and y22. Enumerate all nine possible matings (A1A1 female by A1A1 male, A1A1 female by A1A2 male, etc.) and calculate the frequencies
Page 12 Problem 1.2 Calculate the frequency of the three alkaline phosphatase alleles in the English population. Genotype Number Frequency Expected SS 141 0.4247 0.4096 SF 111 0.3343 0.3507 FF 28 0.0843 0.0751 SI 32 0.0964 0.1101 FI 15 0.0452 0.0471 II 5 0.0151 0.0074 Total 332 1.0000 1.0000 Table 1.2: The frequencies of alkaline
Page 11 Problem 1.1 How many different genotypes are there at a locus with n alleles that differ by state? You already know that there is one genotype at a locus with one allele and three genotypes at a locus with two alleles. Continue this with three, four, and more alleles until you divine the