Download Biological Sequence Analysis Using the SeqAn C++ Library by Andreas Gogol-Döring PDF

By Andreas Gogol-Döring

An Easy-to-Use examine instrument for set of rules checking out and Development

Before the SeqAn venture, there has been essentially a scarcity of obtainable implementations in series research, even for traditional projects. Implementations of wanted algorithmic elements have been both unavailable or not easy to entry in third-party monolithic software program items. Addressing those issues, the builders of SeqAn created a accomplished, easy-to-use, open resource C++ library of effective algorithms and knowledge constructions for the research of organic sequences. Written by means of the founders of this venture, Biological series research utilizing the SeqAn C++ Library covers the SeqAn library, its documentation, and the assisting infrastructure.

The first a part of the ebook describes the final library layout. It introduces organic series research difficulties, discusses the good thing about utilizing software program libraries, summarizes the layout rules and objectives of SeqAn, information the most programming ideas utilized in SeqAn, and demonstrates the appliance of those ideas in numerous examples. targeting the parts supplied by means of SeqAn, the second one half explores simple performance, series info buildings, alignments, development and motif looking, string indices, and graphs. The final half illustrates purposes of SeqAn to genome alignment, consensus series in meeting tasks, suffix array building, and more.

This convenient e-book describes a easy library of effective facts kinds and algorithms for series research in computational biology. SeqAn permits not just the implementation of latest algorithms, but additionally the sound research and comparability of latest algorithms.

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Read or Download Biological Sequence Analysis Using the SeqAn C++ Library (Chapman & Hall CRC Mathematical & Computational Biology) PDF

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Additional info for Biological Sequence Analysis Using the SeqAn C++ Library (Chapman & Hall CRC Mathematical & Computational Biology)

Example text

Relevant is not the type T itself but its interface, and (2) this concept is minimal in the sense that it contains only those requirements that are essential for the data structure or algorithm to work on T. 3). Generic data types and algorithms can be implemented in C++ using templates (ISO/IEC 1998, section 14). A class template parameterizes a class with a list of types or constants. , the type of the values that will be stored in vector. The template is generic, it can be applied to any type T.

2010 by Taylor and Francis Group, LLC 34 Biological Sequence Analysis Using the SeqAn C++ Library container type obj, and this invokes the most suitable implementation of find depending on the type of obj. Listing 2 gives an example of this idea: The map is implemented in the specialization Container of the generic class Container. Since the subclass is specified by choosing a template argument, we call this approach template subclassing. In the lower part of Listing 2, we see different levels of specificity for find algorithms: The first is applicable for any type – therefore we call it the most general function – the second for instances of Container, and the third only for Container objects.

C++ standard strings basic_string. • Zero-terminated char arrays (C-style strings). 47 © 2010 by Taylor and Francis Group, LLC 48 Biological Sequence Analysis Using the SeqAn C++ Library We will need the following functions and metafunctions: The metafunctions Value and ValueSize to determine the value type and the number of different values this type can get, the function length that returns the length of the string, and the function value for accessing the string at a given position. Note that all these functions and metafunctions are already defined in SeqAn; we will discuss how.

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