Efficient methods for inferring tandem duplication history

Louxin Zhang; Bin Ma; Lusheng Wang

doi:10.1007/3-540-45784-4_8

Efficient methods for inferring tandem duplication history

Louxin Zhang, Bin Ma, Lusheng Wang

Department of Computer Science

Research output: Chapters, Conference Papers, Creative and Literary Works › RGC 32 - Refereed conference paper (with host publication) › peer-review

3 Citations (Scopus)

Abstract

In this paper, we study the problem of inferring duplication history of a tandem gene family using the duplication model proposed by Tang et al.. We provide an efficient algorithm for inferring a duplication model for a given set of (gene) sequences by combining a linear-time algorithm, which is for determining whether a rooted tree is associated with a duplication model, with the nearest neighbor interchange operation. Finally, using our proposed method, we derive duplication hypotheses for an exon of a mucin gene MUC5B, a ZNF gene family, and a OR gene family. © Springer-Verlag Berlin Heidelberg 2002

Original language	English
Title of host publication	Algorithms in Bioinformatics
Subtitle of host publication	Second International Workshop, WABI 2002, Rome, Italy, September 17-21, 2002, Proceedings
Editors	Roderic Guigo, Dan Gusfield
Place of Publication	Berlin, Heidelberg
Publisher	Springer
Pages	97-111
ISBN (Electronic)	978-3-540-45784-8
ISBN (Print)	9783540442110
DOIs	https://doi.org/10.1007/3-540-45784-4_8
Publication status	Published - 2002
Event	2nd International Workshop on Algorithms in Bioinformatics (WABI 2002) - Rome, Italy Duration: 17 Sept 2002 → 21 Sept 2002

Publication series

Name	Lecture Notes in Computer Science
Volume	2452
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	2nd International Workshop on Algorithms in Bioinformatics (WABI 2002)
Place	Italy
City	Rome
Period	17/09/02 → 21/09/02

Research Keywords

Algorithm
Mucin genes
Olfactory receptors
Phylogeny
Tandem duplication model
ZNF genes

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10.1007/3-540-45784-4_8

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@inproceedings{3ffca0925c1d4334a8fdbfbc99189ed2,

title = "Efficient methods for inferring tandem duplication history",

abstract = "In this paper, we study the problem of inferring duplication history of a tandem gene family using the duplication model proposed by Tang et al.. We provide an efficient algorithm for inferring a duplication model for a given set of (gene) sequences by combining a linear-time algorithm, which is for determining whether a rooted tree is associated with a duplication model, with the nearest neighbor interchange operation. Finally, using our proposed method, we derive duplication hypotheses for an exon of a mucin gene MUC5B, a ZNF gene family, and a OR gene family. {\textcopyright} Springer-Verlag Berlin Heidelberg 2002",

keywords = "Algorithm, Mucin genes, Olfactory receptors, Phylogeny, Tandem duplication model, ZNF genes",

author = "Louxin Zhang and Bin Ma and Lusheng Wang",

year = "2002",

doi = "10.1007/3-540-45784-4_8",

language = "English",

isbn = "9783540442110",

series = "Lecture Notes in Computer Science",

publisher = "Springer ",

pages = "97--111",

editor = "Roderic Guigo and Dan Gusfield",

booktitle = "Algorithms in Bioinformatics",

note = "2nd International Workshop on Algorithms in Bioinformatics (WABI 2002) ; Conference date: 17-09-2002 Through 21-09-2002",

}

Zhang, L, Ma, B & Wang, L 2002, Efficient methods for inferring tandem duplication history. in R Guigo & D Gusfield (eds), Algorithms in Bioinformatics: Second International Workshop, WABI 2002, Rome, Italy, September 17-21, 2002, Proceedings. Lecture Notes in Computer Science, vol. 2452, Springer , Berlin, Heidelberg, pp. 97-111, 2nd International Workshop on Algorithms in Bioinformatics (WABI 2002), Rome, Italy, 17/09/02. https://doi.org/10.1007/3-540-45784-4_8

Efficient methods for inferring tandem duplication history. / Zhang, Louxin; Ma, Bin; Wang, Lusheng.
Algorithms in Bioinformatics: Second International Workshop, WABI 2002, Rome, Italy, September 17-21, 2002, Proceedings. ed. / Roderic Guigo; Dan Gusfield. Berlin, Heidelberg: Springer , 2002. p. 97-111 (Lecture Notes in Computer Science; Vol. 2452).

Research output: Chapters, Conference Papers, Creative and Literary Works › RGC 32 - Refereed conference paper (with host publication) › peer-review

TY - GEN

T1 - Efficient methods for inferring tandem duplication history

AU - Zhang, Louxin

AU - Ma, Bin

AU - Wang, Lusheng

PY - 2002

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N2 - In this paper, we study the problem of inferring duplication history of a tandem gene family using the duplication model proposed by Tang et al.. We provide an efficient algorithm for inferring a duplication model for a given set of (gene) sequences by combining a linear-time algorithm, which is for determining whether a rooted tree is associated with a duplication model, with the nearest neighbor interchange operation. Finally, using our proposed method, we derive duplication hypotheses for an exon of a mucin gene MUC5B, a ZNF gene family, and a OR gene family. © Springer-Verlag Berlin Heidelberg 2002

AB - In this paper, we study the problem of inferring duplication history of a tandem gene family using the duplication model proposed by Tang et al.. We provide an efficient algorithm for inferring a duplication model for a given set of (gene) sequences by combining a linear-time algorithm, which is for determining whether a rooted tree is associated with a duplication model, with the nearest neighbor interchange operation. Finally, using our proposed method, we derive duplication hypotheses for an exon of a mucin gene MUC5B, a ZNF gene family, and a OR gene family. © Springer-Verlag Berlin Heidelberg 2002

KW - Algorithm

KW - Mucin genes

KW - Olfactory receptors

KW - Phylogeny

KW - Tandem duplication model

KW - ZNF genes

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M3 - RGC 32 - Refereed conference paper (with host publication)

SN - 9783540442110

T3 - Lecture Notes in Computer Science

SP - 97

EP - 111

BT - Algorithms in Bioinformatics

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ER -

Efficient methods for inferring tandem duplication history

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