K-mer similarity: A rapid similarity search algorithm for probe design

Xiao fei Cui; Ya dong Wang; Guang ri Quan; Yong dong Xu

K-mer similarity: A rapid similarity search algorithm for probe design

Xiao fei Cui
, Ya dong Wang
, Guang ri Quan
, Yong dong Xu^*

^*Corresponding author for this work

School of Computer Science and Technology (School of Software), Harbin Institute of Technology Weihai

Research output: Chapter in Book/Report/Conference proceeding › Chapter › peer-review

Abstract

Actual hybridization is performed on a global identity scenario. However, searching for sequences similar to a given sequence in a large data set is very challenging. This is especially true for global alignment. A local alignment algorithm BLAST or semi-global algorithm Myers' bit-vector algorithm is used to instead in most cases. We introduce a novel global alignment method in this paper. It computes the same alignment as a certain dynamic programming algorithm, while executing over 60 times faster on appropriate data. Its high accuracy and speed makes it a better choice for the alignment of probe design.

Original language	English
Title of host publication	Current Trends in Computer Science and Mechanical Automation Vol.1
Subtitle of host publication	Selected Papers from CSMA2016
Publisher	de Gruyter
Pages	9-20
Number of pages	12
ISBN (Electronic)	9783110584974
ISBN (Print)	9783110584967
State	Published - 9 Jan 2018
Externally published	Yes

Keywords

Component
Fast
Global alignment
Probe design

Cite this

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PY - 2018/1/9

Y1 - 2018/1/9

N2 - Actual hybridization is performed on a global identity scenario. However, searching for sequences similar to a given sequence in a large data set is very challenging. This is especially true for global alignment. A local alignment algorithm BLAST or semi-global algorithm Myers' bit-vector algorithm is used to instead in most cases. We introduce a novel global alignment method in this paper. It computes the same alignment as a certain dynamic programming algorithm, while executing over 60 times faster on appropriate data. Its high accuracy and speed makes it a better choice for the alignment of probe design.

AB - Actual hybridization is performed on a global identity scenario. However, searching for sequences similar to a given sequence in a large data set is very challenging. This is especially true for global alignment. A local alignment algorithm BLAST or semi-global algorithm Myers' bit-vector algorithm is used to instead in most cases. We introduce a novel global alignment method in this paper. It computes the same alignment as a certain dynamic programming algorithm, while executing over 60 times faster on appropriate data. Its high accuracy and speed makes it a better choice for the alignment of probe design.

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KW - Fast

KW - Global alignment

KW - Probe design

UR - https://www.scopus.com/pages/publications/85132310065

M3 - 章节

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BT - Current Trends in Computer Science and Mechanical Automation Vol.1

PB - de Gruyter

ER -

K-mer similarity: A rapid similarity search algorithm for probe design

Abstract

Keywords

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