Toona_sinensis platform

I. Introduction

What is Toona_sinensis platform Database?

Toona_sinensis platform Database is a plant database. The Toona_sinensis platform has established a Toona platform database forum to share resources, share new discoveries, exchange research and publish announcements. In the future, we will continue to provide new insights into Meliaceae research for the Toona_sinensis platform database.

 

II. Datasets and Workflow

Data sources

Toona_sinensis 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.

ColinearScan Installation package Download

 

III. FAQ

A. What information does Toona_sinensis platform Database provide for plant Karyotype evolution?

Toona_sinensis shows the evolution history of its chromosomes, vividly shows its evolution history of billions of years, and provides a software download function.

 

B. How to contact us?

If you meet any troubles or find any bugs when you visit Toona_sinensis platform Database, please email to yuzijian1010@163.com, 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

 

IV. Citation

Data files contained in the Toona_sinensis 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: