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Computer Engineering Commons

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Computer Science and Engineering: Theses, Dissertations, and Student Research

Computer Sciences

Algorithms

2018

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Full-Text Articles in Computer Engineering

Application Of Cosine Similarity In Bioinformatics, Srikanth Maturu May 2018

Application Of Cosine Similarity In Bioinformatics, Srikanth Maturu

Computer Science and Engineering: Theses, Dissertations, and Student Research

Finding similar sequences to an input query sequence (DNA or proteins) from a sequence data set is an important problem in bioinformatics. It provides researchers an intuition of what could be related or how the search space can be reduced for further tasks. An exact brute-force nearest-neighbor algorithm used for this task has complexity O(m * n) where n is the database size and m is the query size. Such an algorithm faces time-complexity issues as the database and query sizes increase. Furthermore, the use of alignment-based similarity measures such as minimum edit distance adds an additional complexity to the ...