Algorithms

Download e-book for iPad: Algorithms in Bioinformatics: A Practical Introduction by Wing-Kin Sung

By Wing-Kin Sung

ISBN-10: 1420070339

ISBN-13: 9781420070330

Built from the author’s personal instructing fabric, Algorithms in Bioinformatics: a realistic advent offers an in-depth creation to the algorithmic ideas utilized in bioinformatics. for every subject, the writer truly info the organic motivation and accurately defines the corresponding computational difficulties. He additionally contains unique examples to demonstrate each one set of rules and end-of-chapter routines for college students to familiarize themselves with the themes. Supplementary fabric is offered at http://www.comp.nus.edu.sg/~ksung/algo_in_bioinfo/

This classroom-tested textbook starts off with easy molecular biology ideas. It then describes how one can degree series similarity, offers uncomplicated functions of the suffix tree, and discusses the matter of looking out series databases. After introducing equipment for aligning a number of organic sequences and genomes, the textual content explores purposes of the phylogenetic tree, tools for evaluating phylogenetic timber, the matter of genome rearrangement, and the matter of motif discovering. It additionally covers tools for predicting the secondary constitution of RNA and for reconstructing the peptide series utilizing mass spectrometry. the ultimate bankruptcy examines the computational challenge concerning inhabitants genetics.

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The similarity of a pair of aligned characters can be specified by a matrix δ, where δ(x, y) equals the similarity of x and y for x, y ∈ Σ { }. 1 shows an example of a similarity matrix. 6. The aim of the global alignment problem is to find an alignment A which maximizes (x,y)∈A δ(x, y). Such alignment is called the optimal alignment. There is a one-to-one correspondence between a pair of aligned characters and an edit operation. When a pair of aligned characters are the same, it is called a match; otherwise it is called a mismatch.

Those tools help to cut and break DNA (using restriction enzymes or sonication), to duplicate DNA fragments (using cloning or PCR), to measure the length of DNA (using gel electrophoresis), to detect the existence of certain DNA segments in a sample (using hybridization with probes), and to perform DNA sequencing. This section examines these tools. 2 will discuss mass spectrometry and chromatin immunoprecipitation, respectively. Other biotechnologies exist and readers are referred to the literature for details.

Longest Common Subsequence (LCS): Given two sequences X and Y , a sequence Z is said to be a common subsequence of X and Y if Z is a subsequence of both X and Y . The LCS problem aims to find a maximum-length common subsequence of X and Y . For example, the LCS of “catpaplte” and “xapzpleg” is “apple,” which is of length 5. The LCS of two strings is equivalent to the optimal global alignment with the following scoring function. • score for match = 1 • score for mismatch = −∞ (that is, we don’t allow mismatch) • score for insert/delete = 0 Using the same algorithm for the global alignment, LCS can be computed in O(nm) time.

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Algorithms in Bioinformatics: A Practical Introduction by Wing-Kin Sung


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