GenomeSyn: a bioinformatics tool for visualizing genome synteny and structural variations

Zu-Wen Zhou; Zhi-Guang Yu; Xiao-Ming Huang; Jin-Shen Liu; Yi-Xiong Guo; Ling-Ling Chen; Jia-Ming Song

doi:10.1016/j.jgg.2022.03.013

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GenomeSyn: a bioinformatics tool for visualizing genome synteny and structural variations

doi: 10.1016/j.jgg.2022.03.013

1. State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi 530004, China;
2. College of Stomatology, Guangxi Medical University, Nanning, Guangxi 530021, China;
3. National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China

基金项目:

This research was supported by the National Natural Science Foundation of China (32100526, 31871269), Hubei Provincial Natural Science Foundation of China (2019CFA014), Innovation Project of Guangxi Graduate Education (YCSW2022038) and the starting research grant for High-level Talents from Guangxi University.

详细信息

通讯作者:
Ling-Ling Chen,E-mail:llchen@gxu.edu.cn

Jia-Ming Song,E-mail:jmsong@gxu.edu.cn

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- 文章访问数: 1179
- HTML全文浏览量: 482
- PDF下载量: 107
- 被引次数: 0
出版历程
- 收稿日期: 2022-01-04
- 录用日期: 2022-03-29
- 修回日期: 2022-03-24
- 刊出日期: 2022-04-15

GenomeSyn: a bioinformatics tool for visualizing genome synteny and structural variations

1. State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi 530004, China;
2. College of Stomatology, Guangxi Medical University, Nanning, Guangxi 530021, China;
3. National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China

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摘要

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参考文献(9)

Bayer, P. E., Golicz, A. A., Scheben, A., Batley, J., Edwards, D., 2020. Plant pan-genomes are the new reference. Native Plants 6, 914-920

Darling, A. C., Mau, B., Blattner, F. R., Perna, N. T., 2004. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 14, 1394-1403

Haug-Baltzell, A., Stephens, S. A., Davey, S., Scheidegger, C. E., Lyons, E., 2017. SynMap2 and SynMap3D: web-based whole-genome synteny browsers. Bioinformatics 33, 2197-2198

Lee, J., Lee, D., Sim, M., Kwon, D., Kim, J., Ko, Y., Kim, J., 2018. mySyntenyPortal: an application package to construct websites for synteny block analysis. BMC Bioinf. 19, 216

Li H., 2018. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34, 3094-3100

Marcais, G., Delcher, A. L., Phillippy, A. M., Coston, R., Salzberg, S. L., Zimin, A., 2018. MUMmer4: a fast and versatile genome alignment system. PLoS Comput. Biol. 14, e1005944

Pandey, M., Kushwaha, B., Kumar, R., Srivastava, P., Saroj, S., Singh, M., 2020. Evol2Circos: a web-based tool for genome synteny and collinearity analysis and its visualization in fishes. J. Hered. esaa025

Soderlund, C., Nelson, W., Shoemaker, A., Paterson, A., 2006. SyMAP: a system for discovering and viewing syntenic regions of FPC maps. Genome Res. 16, 1159-1168

Tang, H., Bowers, J. E., Wang, X., Ming, R., Alam, M., Paterson, A. H., 2008. Synteny and collinearity in plant genomes. Science 320, 486-488

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文章访问数: 1179
HTML全文浏览量: 482
PDF下载量: 107
被引次数: 0

留言板

GenomeSyn: a bioinformatics tool for visualizing genome synteny and structural variations

doi: 10.1016/j.jgg.2022.03.013

通讯作者: Ling-Ling Chen,E-mail:llchen@gxu.edu.cn Jia-Ming Song,E-mail:jmsong@gxu.edu.cn

计量

出版历程

GenomeSyn: a bioinformatics tool for visualizing genome synteny and structural variations

计量

出版历程

目录

通讯作者:
Ling-Ling Chen,E-mail:llchen@gxu.edu.cn

Jia-Ming Song,E-mail:jmsong@gxu.edu.cn