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פותח על ידי קלירמאש פתרונות בע"מ -
Cucurbit Genomics Database (CuGenDB): a central portal for comparative and functional genomics of cucurbit crops
Year:
2018
Source of publication :
Nucleic Acids Research
Authors :
בורגר, יוסף
;
.
קציר, נורית
;
.
שפר, ארתור
;
.
תדמור, יעקב
;
.
Volume :
Co-Authors:

Yi Zheng, Shan Wu, Yang Bai, Honghe Sun, Chen Jiao, Shaogui Guo, Kun Zhao, Jose Blanca, Zhonghua Zhang, Sanwen Huang, Yong Xu, Yiqun Weng, Michael Mazourek, Umesh K. Reddy, Kaori Ando, James D McCreight, Xuemei Tang, Yang Liu, James J Giovannoni, Kai-Shu Ling, W Patrick Wechter, Amnon Levi, Jordi Garcia-Mas, Rebecca Grumet, Zhangjun Fei

Facilitators :
From page:
0
To page:
0
(
Total pages:
1
)
Abstract:

The Cucurbitaceae family (cucurbit) includes several economically important crops, such as melon, cucumber, watermelon, pumpkin, squash and gourds. During the past several years, genomic and genetic data have been rapidly accumulated for cucurbits. To store, mine, analyze, integrate and disseminate these large-scale datasets and to provide a central portal for the cucurbit research and breeding community, we have developed the Cucurbit Genomics Database (CuGenDB; http://cucurbitgenomics.org) using the Tripal toolkit. The database currently contains all available genome and expressed sequence tag (EST) sequences, genetic maps, and transcriptome profiles for cucurbit species, as well as sequence annotations, biochemical pathways and comparative genomic analysis results such as synteny blocks and homologous gene pairs between different cucurbit species. A set of analysis and visualization tools and user-friendly query interfaces have been implemented in the database to facilitate the usage of these large-scale data by the community. In particular, two new tools have been developed in the database, a ‘SyntenyViewer’ to view genome synteny between different cucurbit species and an ‘RNA-Seq’ module to analyze and visualize gene expression profiles. Both tools have been packed as Tripal extension modules that can be adopted in other genomics databases developed using the Tripal system.

Note:

Article no. gky944

Related Files :
Cucurbitaceae
Database
Genetics
genomics
information technology
עוד תגיות
תוכן קשור
More details
DOI :
https://doi.org/10.1093/nar/gky944
Article number:
0
Affiliations:
Database:
גוגל סקולר
Publication Type:
מאמר
;
.
Language:
אנגלית
Editors' remarks:
ID:
38612
Last updated date:
02/03/2022 17:27
Creation date:
13/12/2018 14:09
Scientific Publication
Cucurbit Genomics Database (CuGenDB): a central portal for comparative and functional genomics of cucurbit crops

Yi Zheng, Shan Wu, Yang Bai, Honghe Sun, Chen Jiao, Shaogui Guo, Kun Zhao, Jose Blanca, Zhonghua Zhang, Sanwen Huang, Yong Xu, Yiqun Weng, Michael Mazourek, Umesh K. Reddy, Kaori Ando, James D McCreight, Xuemei Tang, Yang Liu, James J Giovannoni, Kai-Shu Ling, W Patrick Wechter, Amnon Levi, Jordi Garcia-Mas, Rebecca Grumet, Zhangjun Fei

Cucurbit Genomics Database (CuGenDB): a central portal for comparative and functional genomics of cucurbit crops

The Cucurbitaceae family (cucurbit) includes several economically important crops, such as melon, cucumber, watermelon, pumpkin, squash and gourds. During the past several years, genomic and genetic data have been rapidly accumulated for cucurbits. To store, mine, analyze, integrate and disseminate these large-scale datasets and to provide a central portal for the cucurbit research and breeding community, we have developed the Cucurbit Genomics Database (CuGenDB; http://cucurbitgenomics.org) using the Tripal toolkit. The database currently contains all available genome and expressed sequence tag (EST) sequences, genetic maps, and transcriptome profiles for cucurbit species, as well as sequence annotations, biochemical pathways and comparative genomic analysis results such as synteny blocks and homologous gene pairs between different cucurbit species. A set of analysis and visualization tools and user-friendly query interfaces have been implemented in the database to facilitate the usage of these large-scale data by the community. In particular, two new tools have been developed in the database, a ‘SyntenyViewer’ to view genome synteny between different cucurbit species and an ‘RNA-Seq’ module to analyze and visualize gene expression profiles. Both tools have been packed as Tripal extension modules that can be adopted in other genomics databases developed using the Tripal system.

Article no. gky944

Scientific Publication
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