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OrthoClusterDB: an online platform for synteny blocks

BACKGROUND: The recent availability of an expanding collection of genome sequences driven by technological advances has facilitated comparative genomics and in particular the identification of synteny among multiple genomes. However, the development of effective and easy-to-use methods for identifyi...

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Autores principales: Ng, Man-Ping, Vergara, Ismael A, Frech, Christian, Chen, Qingkang, Zeng, Xinghuo, Pei, Jian, Chen, Nansheng
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2009
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2711082/
https://www.ncbi.nlm.nih.gov/pubmed/19549318
http://dx.doi.org/10.1186/1471-2105-10-192
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author Ng, Man-Ping
Vergara, Ismael A
Frech, Christian
Chen, Qingkang
Zeng, Xinghuo
Pei, Jian
Chen, Nansheng
author_facet Ng, Man-Ping
Vergara, Ismael A
Frech, Christian
Chen, Qingkang
Zeng, Xinghuo
Pei, Jian
Chen, Nansheng
author_sort Ng, Man-Ping
collection PubMed
description BACKGROUND: The recent availability of an expanding collection of genome sequences driven by technological advances has facilitated comparative genomics and in particular the identification of synteny among multiple genomes. However, the development of effective and easy-to-use methods for identifying such conserved gene clusters among multiple genomes–synteny blocks–as well as databases, which host synteny blocks from various groups of species (especially eukaryotes) and also allow users to run synteny-identification programs, lags behind. DESCRIPTIONS: OrthoClusterDB is a new online platform for the identification and visualization of synteny blocks. OrthoClusterDB consists of two key web pages: Run OrthoCluster and View Synteny. The Run OrthoCluster page serves as web front-end to OrthoCluster, a recently developed program for synteny block detection. Run OrthoCluster offers full control over the functionalities of OrthoCluster, such as specifying synteny block size, considering order and strandedness of genes within synteny blocks, including or excluding nested synteny blocks, handling one-to-many orthologous relationships, and comparing multiple genomes. In contrast, the View Synteny page gives access to perfect and imperfect synteny blocks precomputed for a large number of genomes, without the need for users to retrieve and format input data. Additionally, genes are cross-linked with public databases for effective browsing. For both Run OrthoCluster and View Synteny, identified synteny blocks can be browsed at the whole genome, chromosome, and individual gene level. OrthoClusterDB is freely accessible. CONCLUSION: We have developed an online system for the identification and visualization of synteny blocks among multiple genomes. The system is freely available at .
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spelling pubmed-27110822009-07-16 OrthoClusterDB: an online platform for synteny blocks Ng, Man-Ping Vergara, Ismael A Frech, Christian Chen, Qingkang Zeng, Xinghuo Pei, Jian Chen, Nansheng BMC Bioinformatics Database BACKGROUND: The recent availability of an expanding collection of genome sequences driven by technological advances has facilitated comparative genomics and in particular the identification of synteny among multiple genomes. However, the development of effective and easy-to-use methods for identifying such conserved gene clusters among multiple genomes–synteny blocks–as well as databases, which host synteny blocks from various groups of species (especially eukaryotes) and also allow users to run synteny-identification programs, lags behind. DESCRIPTIONS: OrthoClusterDB is a new online platform for the identification and visualization of synteny blocks. OrthoClusterDB consists of two key web pages: Run OrthoCluster and View Synteny. The Run OrthoCluster page serves as web front-end to OrthoCluster, a recently developed program for synteny block detection. Run OrthoCluster offers full control over the functionalities of OrthoCluster, such as specifying synteny block size, considering order and strandedness of genes within synteny blocks, including or excluding nested synteny blocks, handling one-to-many orthologous relationships, and comparing multiple genomes. In contrast, the View Synteny page gives access to perfect and imperfect synteny blocks precomputed for a large number of genomes, without the need for users to retrieve and format input data. Additionally, genes are cross-linked with public databases for effective browsing. For both Run OrthoCluster and View Synteny, identified synteny blocks can be browsed at the whole genome, chromosome, and individual gene level. OrthoClusterDB is freely accessible. CONCLUSION: We have developed an online system for the identification and visualization of synteny blocks among multiple genomes. The system is freely available at . BioMed Central 2009-06-23 /pmc/articles/PMC2711082/ /pubmed/19549318 http://dx.doi.org/10.1186/1471-2105-10-192 Text en Copyright © 2009 Ng et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Database
Ng, Man-Ping
Vergara, Ismael A
Frech, Christian
Chen, Qingkang
Zeng, Xinghuo
Pei, Jian
Chen, Nansheng
OrthoClusterDB: an online platform for synteny blocks
title OrthoClusterDB: an online platform for synteny blocks
title_full OrthoClusterDB: an online platform for synteny blocks
title_fullStr OrthoClusterDB: an online platform for synteny blocks
title_full_unstemmed OrthoClusterDB: an online platform for synteny blocks
title_short OrthoClusterDB: an online platform for synteny blocks
title_sort orthoclusterdb: an online platform for synteny blocks
topic Database
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2711082/
https://www.ncbi.nlm.nih.gov/pubmed/19549318
http://dx.doi.org/10.1186/1471-2105-10-192
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