DUK - A Fast and Efficient Kmer Based Sequence Matching Tool

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A new tool, DUK, is developed to perform matching task. Matching is to find whether a query sequence partially or totally matches given reference sequences or not. Matching is similar to alignment. Indeed many traditional analysis tasks like contaminant removal use alignment tools. But for matching, there is no need to know which bases of a query sequence matches which position of a reference sequence, it only need know whether there exists a match or not. This subtle difference can make matching task much faster than alignment. DUK is accurate, versatile, fast, and has efficient memory usage. It uses Kmer ... continued below

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Li, Mingkun; Copeland, Alex & Han, James March 21, 2011.

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Description

A new tool, DUK, is developed to perform matching task. Matching is to find whether a query sequence partially or totally matches given reference sequences or not. Matching is similar to alignment. Indeed many traditional analysis tasks like contaminant removal use alignment tools. But for matching, there is no need to know which bases of a query sequence matches which position of a reference sequence, it only need know whether there exists a match or not. This subtle difference can make matching task much faster than alignment. DUK is accurate, versatile, fast, and has efficient memory usage. It uses Kmer hashing method to index reference sequences and Poisson model to calculate p-value. DUK is carefully implemented in C++ in object oriented design. The resulted classes can also be used to develop other tools quickly. DUK have been widely used in JGI for a wide range of applications such as contaminant removal, organelle genome separation, and assembly refinement. Many real applications and simulated dataset demonstrate its power.

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  • DOE JGI User Meeting

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  • Report No.: LBNL-4516E-Poster
  • Grant Number: DE-AC02-05CH11231
  • Office of Scientific & Technical Information Report Number: 1016000
  • Archival Resource Key: ark:/67531/metadc846817

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Office of Scientific & Technical Information Technical Reports

Reports, articles and other documents harvested from the Office of Scientific and Technical Information.

Office of Scientific and Technical Information (OSTI) is the Department of Energy (DOE) office that collects, preserves, and disseminates DOE-sponsored research and development (R&D) results that are the outcomes of R&D projects or other funded activities at DOE labs and facilities nationwide and grantees at universities and other institutions.

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  • March 21, 2011

Added to The UNT Digital Library

  • May 19, 2016, 3:16 p.m.

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  • June 15, 2016, 7:05 p.m.

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Li, Mingkun; Copeland, Alex & Han, James. DUK - A Fast and Efficient Kmer Based Sequence Matching Tool, article, March 21, 2011; Berkeley, California. (digital.library.unt.edu/ark:/67531/metadc846817/: accessed October 20, 2018), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT Libraries Government Documents Department.