COSINE: non-seeding method for mapping long noisy sequences | Zendy

Pegah Tootoonchi Afshar | Zendy; Wing Hung Wong | Zendy

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COSINE: non-seeding method for mapping long noisy sequences

Author(s) -

Pegah Tootoonchi Afshar,

Wing Hung Wong

Publication year - 2017

Publication title -

nucleic acids research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.008

H-Index - 537

eISSN - 1362-4954

pISSN - 0305-1048

DOI - 10.1093/nar/gkx511

Subject(s) - cosine similarity , trigonometric functions , biology , similarity (geometry) , context (archaeology) , algorithm , discrete cosine transform , computer science , range (aeronautics) , pattern recognition (psychology) , sensitivity (control systems) , artificial intelligence , biological system , mathematics , engineering , electronic engineering , paleontology , geometry , image (mathematics) , aerospace engineering

Third generation sequencing (TGS) are highly promising technologies but the long and noisy reads from TGS are difficult to align using existing algorithms. Here, we present COSINE, a conceptually new method designed specifically for aligning long reads contaminated by a high level of errors. COSINE computes the context similarity of two stretches of nucleobases given the similarity over distributions of their short k-mers (k = 3-4) along the sequences. The results on simulated and real data show that COSINE achieves high sensitivity and specificity under a wide range of read accuracies. When the error rate is high, COSINE can offer substantial advantages over existing alignment methods.

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