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CHSMiner: a GUI tool to identify chromosomal homologous segments

BACKGROUND: The identification of chromosomal homologous segments (CHS) within and between genomes is essential for comparative genomics. Various processes including insertion/deletion and inversion could cause the degeneration of CHSs. RESULTS: Here we present a Java software CHSMiner that detects...

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Detalles Bibliográficos
Autores principales: Wang, Zhen, Ding, Guohui, Yu, Zhonghao, Liu, Lei, Li, Yixue
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2009
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2647922/
https://www.ncbi.nlm.nih.gov/pubmed/19146671
http://dx.doi.org/10.1186/1748-7188-4-2
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author Wang, Zhen
Ding, Guohui
Yu, Zhonghao
Liu, Lei
Li, Yixue
author_facet Wang, Zhen
Ding, Guohui
Yu, Zhonghao
Liu, Lei
Li, Yixue
author_sort Wang, Zhen
collection PubMed
description BACKGROUND: The identification of chromosomal homologous segments (CHS) within and between genomes is essential for comparative genomics. Various processes including insertion/deletion and inversion could cause the degeneration of CHSs. RESULTS: Here we present a Java software CHSMiner that detects CHSs based on shared gene content alone. It implements fast greedy search algorithm and rigorous statistical validation, and its friendly graphical interface allows interactive visualization of the results. We tested the software on both simulated and biological realistic data and compared its performance with similar existing software and data source. CONCLUSION: CHSMiner is characterized by its integrated workflow, fast speed and convenient usage. It will be useful for both experimentalists and bioinformaticians interested in the structure and evolution of genomes.
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spelling pubmed-26479222009-02-26 CHSMiner: a GUI tool to identify chromosomal homologous segments Wang, Zhen Ding, Guohui Yu, Zhonghao Liu, Lei Li, Yixue Algorithms Mol Biol Software Article BACKGROUND: The identification of chromosomal homologous segments (CHS) within and between genomes is essential for comparative genomics. Various processes including insertion/deletion and inversion could cause the degeneration of CHSs. RESULTS: Here we present a Java software CHSMiner that detects CHSs based on shared gene content alone. It implements fast greedy search algorithm and rigorous statistical validation, and its friendly graphical interface allows interactive visualization of the results. We tested the software on both simulated and biological realistic data and compared its performance with similar existing software and data source. CONCLUSION: CHSMiner is characterized by its integrated workflow, fast speed and convenient usage. It will be useful for both experimentalists and bioinformaticians interested in the structure and evolution of genomes. BioMed Central 2009-01-15 /pmc/articles/PMC2647922/ /pubmed/19146671 http://dx.doi.org/10.1186/1748-7188-4-2 Text en Copyright © 2009 Wang 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 Software Article
Wang, Zhen
Ding, Guohui
Yu, Zhonghao
Liu, Lei
Li, Yixue
CHSMiner: a GUI tool to identify chromosomal homologous segments
title CHSMiner: a GUI tool to identify chromosomal homologous segments
title_full CHSMiner: a GUI tool to identify chromosomal homologous segments
title_fullStr CHSMiner: a GUI tool to identify chromosomal homologous segments
title_full_unstemmed CHSMiner: a GUI tool to identify chromosomal homologous segments
title_short CHSMiner: a GUI tool to identify chromosomal homologous segments
title_sort chsminer: a gui tool to identify chromosomal homologous segments
topic Software Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2647922/
https://www.ncbi.nlm.nih.gov/pubmed/19146671
http://dx.doi.org/10.1186/1748-7188-4-2
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