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Development Note (Go to Top)

PTGBase runs on CentOS server hosted in Department of Genomics and Molecular Biology, Oil Crops Rsearch Institute, Chinase Academy of Agricultural Sciences. The datasets are stored in a relational database powered by MySQL 5.0. The web interface is developed by Perl/CGI, Python, and JavaScript.

The server development, administrations and module installations are supported by Jingyin Yu.



Collaboration Note (Go to Top)
Collaborators Contribution
Wei Hua Principle Investigator.
Jingyin Yu Developed database, Prepared datasets, Prepared the manuscript.
Tao Ke Prepared the annotation data, Prepared the manuscript.
Sadia Tehrim Prepared the manuscript.
Fengming Sun, Wenbin Liu Graphical view.
Data Source (Go to Top)
Latin Name Common Name Data Source
Arabidopsis lyrata Lyrate rockcress
Arabidopsis thaliana Arabidopsis
Aureococcus anophagefferens Heterokont algae
Brachypodium distachyon Purple false brome
Brassica oleracea Cabbage
Brassica rapa Chinese cabbage
Cajanus cajan Pigeonpea
Carica papaya Papaya
Chlamydomonas reinhardtii Green algae
Chlorella variabilis NC64A Microalgae
Cicer arietinum Chickpea
Citrus sinensis Orange
Citrullus lanatus Watermelon
Cucumis sativus Cucumber
Fragaria vesca Strawberry
Glycine max Soybean
Gossypium raimondii Cotton
Linum usitatissimum Flax
Lotus japonicus Lotus
Malus × domestica Borkh. Apple
Medicago truncatula Barrel medic
Musa acuminata Banana
Oryza sativa L. ssp.japonica Rice
Phaeodactylum tricornutum Diatom algae
Physcomitrella pattens Moss
Populus trichocarpa Western poplar
Prunus mume Plum flower
Ricinus communis Castor bean
Selaginella moellendorffii  Selaginella 
Sesamum indicum Sesame
Setaria italica Millet
Solanum lycopersicum Tomato
Solanum tuberosum Potato
Sorghum bicolor Sorghum
Thellugiella parvula Rockface star-violet
Theobroma cacao Cacao
Vitis vinifera Grape vine
Volvox carteri Green alga
Zea mays ssp. mays L. Maize
Method (Go to Top)

I. Firstly for the selection of target species, homologous gene pairs were detected via an automated search algorithm based on an all-against-all BLAST search using protein sequences with strict parameter( E-value cutoff ≤ 1e-20).

II. Second, based on GFF file of target species, target gene models were sorted by descending order according to the gene location on chromosomes.

III. Third, both BLAST result and sorted GFF file were used to detect distance between the two mutually adjacent genes; for two genes located on different pseudomolecular chromosome or chromosome, the distance between the two genes was set to 1. If they are the same gene shown in BLAST result, the distance between the gene and its own was set to 0. Except that, the distances between the two mutually adjacent genes was normalized firstly and make its value fell between 0 and 1.

IV. Fourth, hierarchical clustering algorithm was employed to cluster the tandem repeat genes into groups according to distance threshold between different groups; for two identical groups , their distance between different groups was set to 0, for entirely different groups, the distance was set to 1. The value of distance threshold was assigned from 0 to 1.

Manual (Go to Top)
Home Page
  • Home: About PTGBase; Data sources; News in PTGBase; Acknowledgements and Contact.
  • Browse: Browse species which is collected in PTGBase by alphabetical and taxonomy respectively.
  • Search: Users can search tandem repeat gene by gene ID and search tandem array by gene ID, cluster name, gene number, species name, Gene Ontology term and InterPro accession.
  • BLAST: Users can pasta DNA or peptide sequences to BLAST with CDS or protein sequences of species which is collected in PTGBase.
  • Statistics: Numbers of tandem repeat genes among different species in PTGBase.
  • Download: Users can download tandem array, coding sequences and protein sequences of tandem duplciated genes that collected in PTGBase, as well as genome data of plant species which contained in PTGBase.
  • Document: Important websites and reference paper.
  • Help: Manul for PTGBase.
Browse Page
  • A: Users can browse Species which is collected in PTGBase that sorted by alphabetical and taxonomy respectively.
  • B: Tandem array of species is displayed by cluster name and tandem repeat genes were also displayed.
  • C: Users can browse tandem array for tandem repeat gene list, distribution on chromosome or pseudomolecular chromosome and functional description of tandem repeat genes
  • D: Detail information of tandem repeat gene is displayed, users can extract basic information, putative function and sequences of tandem repeat gene.
Search Page
Through searching page, users can get basic information of tandem repeat genes by gene name and can also obtain tandem array by gene ID, cluster name, gene number, species name, Gene Ontology term and InterPro accession respectively.
This database is currently maintained by Jingyin Yu.

The Key Laboratory of Oil Crops Biology and Genetic Breeding, the Ministry of Agriculture, Oil Crops Research Institute, the Chinese Academy of Agricultural Sciences, Wuhan 430062, China