Cucurbitales platform
I. Introduction
What is Cucurbitales platform Database?
Cucurbitales platform Database is a plant database. The Cucurbitales platform database provides data resources for three species for use by other researchers. In addition, the collinearity between pineapple and other species was analyzed and quantified using 24,283 collinear gene pairs, and similarity comparisons were performed using nucleic acid and protein comparison banks of five species. The Cucurbitales platform database features five new tools for in-depth data mining and experimental practices that facilitate the transition from data acquisition to a full-featured knowledge base. In addition, the Cucurbitales platform database forum was established to share resources, share new discoveries, exchange research and make announcements. We are confident that the Cucurbitales platform database will continue to provide new insights into Solanales research.
II. Datasets and Workflow
Data sources
Cucurbitales platform Database contains CDS, PEP, GFF3 for 3 plant species. Genome-wide literature and gene annotations are available for download at Ascensialy of NCBI (https://www.ncbi.nlm.nih.gov/assembly/) and/or Phytozome V12.1 (https://phytozome.jgi.doe.gov/pz/portal.html).
Data analysis pipelines
Data pre-processing. The format of cdS, PEP, and GFF3 datasets from NCBI is not uniform. The NCBI raw data is processed using python and perl scripts, species_data the data in the module, which is processed data, which facilitates subsequent analysis.
Syntenic analysis. The synthesis of collinear lists is performed using ColinearScan. First, the protein-coding genes and GFF (General Signature Format) files that have already been processed are used. Subsequently, protein-coding sequences are used as queries for intraspecific and interspecific searches using BLAST with an E value of 1e-10. Search all genetic and GFF files and BLAST for comparison results. Import all genes and GFF files and BLAST output files into ColinearScan to scan collinear pairs. After Excel processing, it becomes a collinear list.
III. Tools
Community and collection of resources about genome
|
Items |
Brief Introduction |
Records |
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An online community for plant Karyotype research community |
- |
|
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Collection of commonly used nucl and prot databases |
5 |
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Collinear list gene pairs |
24,283 |
IV. FAQ
A. What information does Cucurbitales platform Database provide for plant Karyotype evolution?
The Cucurbitales platform database contains data from five species, with sequenced whole genomes and colinear gene pairs available for understanding. The Cucurbitales platform database processes raw data across three species and is available for free download.
B. How to download the data in Cucurbitales platform Database?
All data in Cucurbitales platform Database are access to download in Download Page.
C. How to contact us?
If you meet any troubles or find any bugs when you visit Cucurbitales platform Database, please email to [email protected], pull requests in PmiREN Community or you can contact us by:
Address info 21 Bohai Road,Caofeidian, Tangshan 063210, Hebei, China
Tel: +86-0315-8805607
V. Citation
Data files contained in the Cucurbitales platform Database are free of all copyright restrictions and made fully and freely available for non-commercial use. Users of the data should cite the following articles: