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OrthoCluster: a new tool for mining synteny blocks and applications in comparative genomics

Authors:

Matthew J. Nesbitt,

Ismael A. Vergara,

Nansheng ChenAuthors Info & Claims

EDBT '08: Proceedings of the 11th international conference on Extending database technology: Advances in database technology

Pages 656 - 667

https://doi.org/10.1145/1353343.1353423

Published: 25 March 2008 Publication History

Abstract

By comparing genomes among both closely and distally related species, comparative genomics analysis characterizes structures and functions of different genomes in both conserved and divergent regions. Synteny blocks, which are conserved blocks of genes on chromosomes of related species, play important roles in comparative genomics analysis. Although a few tools have been designed to identify synteny blocks, most of them cannot handle some challenging application requirements, particularly the strandedness of genes, gene inversions, gene duplications, and comparison of more than two genomes. We developed a data mining tool, Ortho-Cluster, which can handle all those challenges. It is publicly available at http://genome.sfu.ca/projects/orthocluster. OrthoCluster takes the annotated gene sets of candidate genomes and pairwise orthologous relationships as input and efficiently identifies the complete set of synteny blocks. In addition, OrthoCluster identifies four types of genome rearrangement events namely inversion, transposition, insertion/deletion, and reciprocal translocation. To be fleexible in various application scenarios, OrthoCluster comes with a systematic set of parameters such as the synteny block size, number of mismatches allowed, whether the strandedness is enforced, whether gene ordering is preserved. Furthermore, OrthoCluster can be used to identify segmental duplication in a genome. In this paper, we introduce the major technical ideas, and present some interesting findings using OrthoCluster.

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Cited By

Bandi VGutwin CSiri JNeufeld ESharpe AParkin I(2022)Visualization Tools for Genomic ConservationPlant Bioinformatics10.1007/978-1-0716-2067-0_16(285-308)Online publication date: 1-Jan-2022
https://doi.org/10.1007/978-1-0716-2067-0_16
Ovens KMaleki FEames BMcQuillan I(2021)Juxtapose: a gene-embedding approach for comparing co-expression networksBMC Bioinformatics10.1186/s12859-021-04055-122:1Online publication date: 16-Mar-2021
https://doi.org/10.1186/s12859-021-04055-1
Lallemand TLeduc MLandès CRizzon CLerat E(2020)An Overview of Duplicated Gene Detection Methods: Why the Duplication Mechanism Has to Be Accounted for in Their ChoiceGenes10.3390/genes1109104611:9(1046)Online publication date: 4-Sep-2020
https://doi.org/10.3390/genes11091046
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Index Terms

OrthoCluster: a new tool for mining synteny blocks and applications in comparative genomics
1. Applied computing
  1. Life and medical sciences
2. Information systems
  1. Information systems applications
    1. Data mining

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cover image ACM Other conferences

EDBT '08: Proceedings of the 11th international conference on Extending database technology: Advances in database technology

March 2008

762 pages

ISBN:9781595939265

DOI:10.1145/1353343

Conference Chair:
Noureddine Mouaddib,
General Chair:
Patrick Valduriez,
Program Chairs:
Alfons Kemper
Technische Universität München, Germany
,
Mokrane Bouzeghoub,
Volker Markl,
Laurent Amsaleg,
Ioana Manolescu,
Publications Chair:
Jens Teubner

Copyright © 2008 ACM.

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Published: 25 March 2008

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EDBT '08

EDBT '08: 11th International Conference on Extending Database Technology

March 25 - 29, 2008

Nantes, France

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Overall Acceptance Rate 7 of 10 submissions, 70%

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Cited By

Bandi VGutwin CSiri JNeufeld ESharpe AParkin I(2022)Visualization Tools for Genomic ConservationPlant Bioinformatics10.1007/978-1-0716-2067-0_16(285-308)Online publication date: 1-Jan-2022
https://doi.org/10.1007/978-1-0716-2067-0_16
Ovens KMaleki FEames BMcQuillan I(2021)Juxtapose: a gene-embedding approach for comparing co-expression networksBMC Bioinformatics10.1186/s12859-021-04055-122:1Online publication date: 16-Mar-2021
https://doi.org/10.1186/s12859-021-04055-1
Lallemand TLeduc MLandès CRizzon CLerat E(2020)An Overview of Duplicated Gene Detection Methods: Why the Duplication Mechanism Has to Be Accounted for in Their ChoiceGenes10.3390/genes1109104611:9(1046)Online publication date: 4-Sep-2020
https://doi.org/10.3390/genes11091046
Simonaitis PChateau ASwenson K(2019)A general framework for genome rearrangement with biological constraintsAlgorithms for Molecular Biology10.1186/s13015-019-0149-414:1Online publication date: 19-Jul-2019
https://doi.org/10.1186/s13015-019-0149-4
Simonaitis PSwenson K(2018)Finding local genome rearrangementsAlgorithms for Molecular Biology10.1186/s13015-018-0127-213:1Online publication date: 4-May-2018
https://doi.org/10.1186/s13015-018-0127-2
Pulicani SSimonaitis PRivals ESwenson K(2017)Rearrangement Scenarios Guided by Chromatin StructureComparative Genomics10.1007/978-3-319-67979-2_8(141-155)Online publication date: 15-Sep-2017
https://doi.org/10.1007/978-3-319-67979-2_8
Rajendrakumar P(2017)Synteny with Allied and Model GenomesThe Sorghum Genome10.1007/978-3-319-47789-3_6(117-136)Online publication date: 19-Jan-2017
https://doi.org/10.1007/978-3-319-47789-3_6
Arjona-Medina JTrelles O(2016)Computational Synteny Block: A Framework to Identify Evolutionary EventsIEEE Transactions on NanoBioscience10.1109/TNB.2016.255415015:4(343-353)Online publication date: Jun-2016
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Niehaus EMünsterkötter MProctor RBrown DSharon AIdan YOren-Young LSieber CNovák OPěnčík ATarkowská DHromadová KFreeman SMaymon MElazar MYoussef SEl-Shabrawy EShalaby AHouterman PBrock NBurkhardt ITsavkelova EDickschat JGaluszka PGüldener UTudzynski B(2016) Comparative “Omics” of the Fusarium fujikuroi Species Complex Highlights Differences in Genetic Potential and Metabolite Synthesis Genome Biology and Evolution10.1093/gbe/evw2598:11(3574-3599)Online publication date: 31-Dec-2016
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Arjona-Medina JTrelles O(2015)Computational Synteny BlockProceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)10.1109/BIBM.2015.7359648(5-12)Online publication date: 9-Nov-2015
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