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

By Andreas Gogol-Döring

An Easy-to-Use examine software for set of rules trying out and Development

Before the SeqAn undertaking, there has been essentially a scarcity of accessible implementations in series research, even for normal projects. Implementations of wanted algorithmic parts 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 information constructions for the research of organic sequences. Written by way of the founders of this undertaking, Biological series research utilizing the SeqAn C++ Library covers the SeqAn library, its documentation, and the aiding 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 ideas and targets of SeqAn, information the most programming innovations utilized in SeqAn, and demonstrates the applying of those suggestions in a variety of examples. targeting the parts supplied by means of SeqAn, the second one half explores simple performance, series information buildings, alignments, development and motif looking, string indices, and graphs. The final half illustrates functions of SeqAn to genome alignment, consensus series in meeting initiatives, suffix array development, and more.

This convenient e-book describes a trouble-free library of effective information forms and algorithms for series research in computational biology. SeqAn permits not just the implementation of recent algorithms, but in addition the sound research and comparability of latest algorithms.

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An Easy-to-Use learn device for set of rules trying out and DevelopmentBefore the SeqAn undertaking, there has been sincerely a scarcity of accessible implementations in series research, even for traditional initiatives. Implementations of wanted algorithmic parts have been both unavailable or not easy to entry in third-party monolithic software program items.

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Sample text

For that reason, we implemented a simple but powerful built-system that allows the compilation of applications and test programs using different compilers and operating systems. Our library now works on all common platforms, namely Microsoft Windows, Mac OS X, Solaris, and several Linux clones, and it was tested for Microsoft Visual C++ compilers (version 7 or above) and GCC compilers (version 3 or above). 4 This license allows the free use and distribution of the library also for commercial use.

Plain interfaces improve a library’s usability and accessibility, make it easier for a potential user to evaluate the usefulness of the library, and reduce the training needed to use it. In addition the internal mechanisms of a library should never get too complex, since this would slow down the development process of the library, complicate its maintenance, and it could be a source of hidden errors. A user of the library will become a victim of exotic compiler behavior, unreadable error messages, or inconsistencies in the language standard to the same extent the library uses elaborated language features.

In the spirit of the object-oriented terminology we can say that the class Container was derived from the general class Container, since all algorithms that are defined for Container also work for Container and are therefore inherited. Let us compare this to object-oriented programming: The method find is inherited from the base class Container to all derived classes, but it was overloaded for the class Map which defines its own find method. 2 but a member function. find(), which differs completely from the application of the generic algorithm that would be called by find(obj).

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