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 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