Circular sequence comparison: algorithms and applications
نویسندگان
چکیده
منابع مشابه
Circular Sequence Comparison with q-grams
Sequence comparison is a fundamental step in many important tasks in bioinformatics. Traditional algorithms for measuring approximation in sequence comparison are based on the notions of distance or similarity, and are generally computed through sequence alignment techniques. As circular genome structure is a common phenomenon in nature, a caveat of specialized alignment techniques for circular...
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The fact that biological sequences can be represented as strings belonging to a finite alphabet (A, C, G, and T for DNA) plays an important role in connecting biology to computer science. String representation allows researchers to apply various string comparison techniques available in computer science. As a result, various applications have been developed that facilitate the task of sequence ...
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Pair-wise sequence alignment is the basic method of comparative analysis of proteins and nucleic acids. Studying the results of the alignment one has to consider two questions: (1) did the program find all the interesting similarities (“sensitivity”) and (2) are all the found similarities interesting (“selectivity”). Definitely, one has to specify, what alignments are considered as the interest...
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We surveyed several important formulations of the sequence database search problem (i.e. local sequence alignment) as well as their solutions. These include the Maximal Segment Pair (MSP) formulation, which has a trivial dynamic programming solution and serve as the basis for popular heuristic solutions such as BLAST 2] and FASTA 18]. The local alignment with gaps formulation as well as a restr...
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ژورنال
عنوان ژورنال: Algorithms for Molecular Biology
سال: 2016
ISSN: 1748-7188
DOI: 10.1186/s13015-016-0076-6