New lightweight index SUA for biological sequence analysis

Di Wang; Guoren Wang; Baichen Chen; Qingquan Wu; Bin Wang; Donghong Han

New lightweight index SUA for biological sequence analysis

Di Wang^*, Guoren Wang, Baichen Chen, Qingquan Wu, Bin Wang, Donghong Han

^*Corresponding author for this work

Northeastern University China

Research output: Contribution to journal › Article › peer-review

6 Citations (Scopus)

Abstract

Searching for repetitions is an important topic in bio-sequence analysis but the bottleneck of current indices used for it such as suffix tree is much too huge space consumption. Succeeding unit array (SUA), a lightweight index structure, is proposed through the analysis of repetitions in the DNA sequences in order to solve the bottleneck. It is constructed based on Radix sorting. Furthermore, SUA is suitable for multi-sequences analysis. The theoretical analysis shows the advantage of SUA in space consumption. Given a sequence of length n, the space consumption of SUA is only about 5 n in the experiments. Meanwhile, the construction is faster than other indices such as suffix tree.

Original language	English
Pages (from-to)	209-212+225
Journal	Huazhong Keji Daxue Xuebao (Ziran Kexue Ban)/Journal of Huazhong University of Science and Technology (Natural Science Edition)
Volume	33
Issue number	SUPPL.
Publication status	Published - Dec 2005
Externally published	Yes

Keywords

DNA sequences
Repetition
SUA

Cite this

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title = "New lightweight index SUA for biological sequence analysis",

abstract = "Searching for repetitions is an important topic in bio-sequence analysis but the bottleneck of current indices used for it such as suffix tree is much too huge space consumption. Succeeding unit array (SUA), a lightweight index structure, is proposed through the analysis of repetitions in the DNA sequences in order to solve the bottleneck. It is constructed based on Radix sorting. Furthermore, SUA is suitable for multi-sequences analysis. The theoretical analysis shows the advantage of SUA in space consumption. Given a sequence of length n, the space consumption of SUA is only about 5 n in the experiments. Meanwhile, the construction is faster than other indices such as suffix tree.",

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author = "Di Wang and Guoren Wang and Baichen Chen and Qingquan Wu and Bin Wang and Donghong Han",

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T1 - New lightweight index SUA for biological sequence analysis

AU - Wang, Di

AU - Wang, Guoren

AU - Chen, Baichen

AU - Wu, Qingquan

AU - Wang, Bin

AU - Han, Donghong

PY - 2005/12

Y1 - 2005/12

N2 - Searching for repetitions is an important topic in bio-sequence analysis but the bottleneck of current indices used for it such as suffix tree is much too huge space consumption. Succeeding unit array (SUA), a lightweight index structure, is proposed through the analysis of repetitions in the DNA sequences in order to solve the bottleneck. It is constructed based on Radix sorting. Furthermore, SUA is suitable for multi-sequences analysis. The theoretical analysis shows the advantage of SUA in space consumption. Given a sequence of length n, the space consumption of SUA is only about 5 n in the experiments. Meanwhile, the construction is faster than other indices such as suffix tree.

AB - Searching for repetitions is an important topic in bio-sequence analysis but the bottleneck of current indices used for it such as suffix tree is much too huge space consumption. Succeeding unit array (SUA), a lightweight index structure, is proposed through the analysis of repetitions in the DNA sequences in order to solve the bottleneck. It is constructed based on Radix sorting. Furthermore, SUA is suitable for multi-sequences analysis. The theoretical analysis shows the advantage of SUA in space consumption. Given a sequence of length n, the space consumption of SUA is only about 5 n in the experiments. Meanwhile, the construction is faster than other indices such as suffix tree.

KW - DNA sequences

KW - Repetition

KW - SUA

UR - https://www.scopus.com/pages/publications/33644641047

M3 - Article

AN - SCOPUS:33644641047

SN - 1671-4512

VL - 33

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JO - Huazhong Keji Daxue Xuebao (Ziran Kexue Ban)/Journal of Huazhong University of Science and Technology (Natural Science Edition)

JF - Huazhong Keji Daxue Xuebao (Ziran Kexue Ban)/Journal of Huazhong University of Science and Technology (Natural Science Edition)

IS - SUPPL.

ER -

New lightweight index SUA for biological sequence analysis

Abstract

Keywords

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