| Glossary List of terms used in SeqAn Adaption Functionality that allows to access built-in type or data types from external libraries in the same way as SeqAn classes. See: Adaptions Affine Gap Costs A scoring scheme that defines the score for a gap of length n as gap_open + (n-1)* gap_extend. See: Linear Gap Costs, Scoring Scheme Alignment An arrangement of two or more sequences: Each character is connected to at most one character for each other sequence, and that the characters in each sequence are ordered in the same way as the connected characters in other sequences. See: Align, Alignment Graph Blank One position within a gap area of an alignment. Concept A kind of interface used in generic programmic that is not formulated in C++ but only a part of the documentation. See: Concepts Gap A part of an alignment in which characters of one sequence are not aligned to characters of the other sequence. Haystack The sequence that is searched for needles. See: Finder Index A data structure for faster searching in sequences. See: Index Linear Gap Costs A scoring scheme that defines the score for a gap to be proportional to the length of the gap. See: Scoring Scheme Metafunction A C++ construct that is used to determine types and constants at compile time. See: Introduction to Metafunctions, Metafunctions Needle The sequence that is searched in the haystack. See: Pattern Scoring Scheme A rule for calculating the similarity between two values or between a value and a blank. Scoring schemes are used for searching and aligning. In SeqAn, scoring schemes are stored in score objects, e.g. Simple Score or Pam120. See: Score SeqAn The C++ library for sequence analysis. You are just reading the documentation of this library. For more information see http://www.seqan.de. See: SeqAn - The Library for Sequence Analysis - Documentation Specialization A refinement of a class that was defined using Template Subclassing. See: Specializations Tag A type that acts as a switch when applied as argument to functions or metafunctions. See: Tags Template Subclassing An alternative to inheritance for the refinement of classes that is based on class template specialization. See: Introduction to Template Subclassing Trie A tree shaped automaton. See: Trie SeqAn - Sequence Analysis Library - www.seqan.de

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