By Andreas Gogol-Döring

ISBN-10: 142007623X

ISBN-13: 9781420076233

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

Before the SeqAn undertaking, there has been basically an absence of obtainable implementations in series research, even for traditional initiatives. Implementations of wanted algorithmic elements have been both unavailable or demanding to entry in third-party monolithic software program items. Addressing those matters, the builders of SeqAn created a finished, easy-to-use, open resource C++ library of effective algorithms and information buildings for the research of organic sequences. Written through the founders of this undertaking, Biological series research utilizing the SeqAn C++ Library covers the SeqAn library, its documentation, and the helping infrastructure.

The first a part of the publication describes the final library layout. It introduces organic series research difficulties, discusses the advantage of utilizing software program libraries, summarizes the layout rules and targets of SeqAn, info the most programming thoughts utilized in SeqAn, and demonstrates the applying of those suggestions in quite a few examples. targeting the elements supplied by way of SeqAn, the second one half explores easy performance, series information buildings, alignments, trend 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 ebook describes a ordinary library of effective info varieties and algorithms for series research in computational biology. SeqAn allows not just the implementation of latest algorithms, but additionally the sound research and comparability of current algorithms.

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

Example text

The string) and that thereby does not rely on members of the input type, but instead uses some kind of global interface. Such task can be performed by metafunctions, also known as type traits (Vandevoorde and Josuttis 2002, chapter 15). A metafunction is a construct to map some types or constants to other entities like types, constants, functions, or objects at compile time. We use class templates to implement metafunctions in C++. Listing 4 shows an example for the definition and application of a metafunction Value for determining the value type of containers.

The screen shot shows a list of messages and issues posted by SeqAn users from around the world. program compiles correctly even if some templates contain syntax errors, just because these templates are never instantiated. We therefore apply a white-box testing method that ensures each template function to be instantiated at least once in the test. This is done by inserting the preprocessor macro SEQAN_CHECKPOINT at the beginning of each template function of the library, and maybe also in some further parts of the program for which we want to check that they are reached by the test.

1. Moreover, SeqAn defines several shortcuts for frequently used classes. For example, we defined the type DnaString as a shortcut for String and DnaIterator for the iterator Iterator::Type of DnaString. This way it is possible to program basic tasks in SeqAn even without explicitly defining any template arguments. © 2010 by Taylor and Francis Group, LLC 46 Biological Sequence Analysis Using the SeqAn C++ Library struct NeedlemanWunsch; struct Hirschberg; template void globalAlignment(TAlignment & ali, TScoring const & scoring, NeedlemanWunsch) { //Needleman-Wunsch algorithm } template void globalAlignment(TAlignment & ali, TScoring const & scoring, Hirschberg) { //Hirschberg’s algorithm } Listing 6: Tag Dispatching Example.

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Biological Sequence Analysis Using the SeqAn C++ Library (Chapman & Hall CRC Mathematical & Computational Biology) by Andreas Gogol-Döring

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