Cucurbitales Genome Research Platform
I. Introduction
What is Cucurbitales Genome Research Platform (CGRP)?
CGRP is a Cucurbitales genome research and analysis platform. The Cucurbitales genome research platform provides data resources for 14 species for use by other researchers. By using comparative genomics methods, polyploidization events and event related genes in the Oleaceae family have been identified. The platform collects transcriptome, genome TE, Identification of relevant functional genes, gene annotation, transcription factor identification, GO and KEGG identification of 14 Cucurbitales species, and makes appropriate analysis. The platform provides good technical support for the classification of important trait genes and gene family of Cucurbitales. CGRP provides three comparative genomics analysis pipelines for deep data mining and experimental practice, containing 37 analytical tools that facilitate comparative genomics. We are confident that the Cucurbitales genome research platform will continue to provide new insights into Cucurbitales research.
II. Datasets and Workflow
Data sources
The Cucurbitales genome research platform contains three plant data: CDS, PEP and GFF3. 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
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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 Genome Research Platform provide for plant Karyotype evolution?
The Cucurbitales Genome Research Platform contains data from five species, with sequenced whole genomes and colinear gene pairs available for understanding. The Cucurbitales Genome Research Platform processes raw data across three species and is available for free download.
B. How to download the data in Cucurbitales Genome Research Platform?
All data in Cucurbitales Genome Research Platform 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 Genome Research Platform, 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 Genome Research Platform 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: