Minimally overlapping words for sequence similarity search | Zendy

Martin C. Frith | Zendy; Laurent Noé | Zendy; Grégory Kucherov | Zendy

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Minimally overlapping words for sequence similarity search

Author(s) -

Martin C. Frith,

Laurent Noé,

Grégory Kucherov

Publication year - 2020

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btaa1054

Subject(s) - computer science , similarity (geometry) , simple (philosophy) , sequence (biology) , seeding , software , artificial intelligence , boosting (machine learning) , sensitivity (control systems) , nearest neighbor search , pattern recognition (psychology) , algorithm , biology , genetics , image (mathematics) , epistemology , electronic engineering , agronomy , programming language , engineering , philosophy

Analysis of genetic sequences is usually based on finding similar parts of sequences, e.g. DNA reads and/or genomes. For big data, this is typically done via 'seeds': simple similarities (e.g. exact matches) that can be found quickly. For huge data, sparse seeding is useful, where we only consider seeds at a subset of positions in a sequence.

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