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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...
Autores principales: | , , , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2009
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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. |
format | Text |
id | pubmed-2647922 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2009 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
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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