Approximate similarity search in genomic sequence databases using landmark-guided embedding

Date

2008-04-12

Author

Sacan, Ahmet
Toroslu, İsmail Hakkı

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This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

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Similarity search in sequence databases is ofparamount importance in bioinformatics research. As the size of the genomic databases increases, similarity search of proteins in these databases becomes a bottle-neck in large-scale studies, calling for more efficient methods of content-based retrieval. In this study, we present a metric-preserving, landmark-guided embedding approach to represent sequences in the vector domain in order to allow efficient indexing and similarity search. We analyze various properties of the embedding and show that the approximation achieved by the embedded representation is sufficient to achieve biologically relevant results. The approximate representation is shown to provide several orders of magnitude speed-up in similarity search compared to the exact representation, while maintaining comparable search accuracy.

Subject Keywords

Genomics, Bioinformatics, Databases, Sequences, Indexing, Matrices, Proteins, Data engineering, Large-scale systems, Computer science

URI

https://hdl.handle.net/11511/45983

DOI

https://doi.org/10.1109/icdew.2008.4498343

Collections

Department of Computer Engineering, Conference / Seminar

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Citation Formats

A. Sacan and İ. H. Toroslu, “Approximate similarity search in genomic sequence databases using landmark-guided embedding,” 2008, Accessed: 00, 2020. [Online]. Available: https://hdl.handle.net/11511/45983.