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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 ftp://ftp.jgi-psf.org/pub/JGI_data/phytozome/v7.0/Alyrata/
Arabidopsis thaliana Arabidopsis http://www.arabidopsis.org
Aureococcus anophagefferens Heterokont algae http://genome.jgi-psf.org/Auran1/Auran1.download.ftp.html
Brachypodium distachyon Purple false brome http://files.brachypodium.org/Annotation/
Brassica oleracea Cabbage http://ocri-genomics.org/bolbase
Brassica rapa Chinese cabbage http://brassicadb.org/brad/
Cajanus cajan Pigeonpea http://www.icrisat.org
Carica papaya Papaya ftp://asgpb.mhpcc.hawaii.edu/papaya/annotation/
Chlamydomonas reinhardtii Green algae ftp://ftp.jgi-psf.org/pub/JGI_data/phytozome/v7.0/Creinhardtii
Chlorella variabilis NC64A Microalgae  http://genome.jgi-psf.org/ChlNC64A_1/ChlNC64A_1.download.ftp.html
Cicer arietinum Chickpea http://www.coolseasonfoodlegume.org/C_arietinum
Citrus sinensis Orange http://citrus.hzau.edu.cn/orange/download/data.php
Citrullus lanatus Watermelon http://www.icugi.org/cgi-bin/ICuGI/index.cgi
Cucumis sativus Cucumber http://cucumber.genomics.org.cn/page/cucumber/index.jsp
Fragaria vesca Strawberry https://strawberry.plantandfood.co.nz/gbrowse/navbar/strawberry/download.html
Glycine max Soybean http://genome.jgi-psf.org/soybean/soybean.home.html
Gossypium raimondii Cotton http://cgp.genomics.org.cn/
Linum usitatissimum Flax http://www.linum.ca
Lotus japonicus Lotus ftp://ftp.kazusa.or.jp/pub/lotus/
Malus × domestica Borkh. Apple http://www.rosaceae.org/projects/apple_genome
Medicago truncatula Barrel medic http://www.medicago.org/
Musa acuminata Banana http://banana-genome.cirad.fr/
Oryza sativa L. ssp.japonica Rice http://rice.plantbiology.msu.edu/index.shtml
Phaeodactylum tricornutum Diatom algae http://genome.jgi-psf.org/Phatr2/Phatr2.info.html
Physcomitrella pattens Moss http://genome.jgi-psf.org/Phypa1_1/Phypa1_1.download.html
Populus trichocarpa Western poplar http://genome.jgi-psf.org/Poptr1_1/Poptr1_1.home.html
Prunus mume Plum flower http://prunusmumegenome.bjfu.edu.cn/
Ricinus communis Castor bean http://castorbean.jcvi.org/downloads.php
Selaginella moellendorffii  Selaginella http://genome.jgi.doe.gov/Selmo1/Selmo1.download.ftp.html 
Sesamum indicum Sesame http://ocri-genomics.org/Sinbase
Setaria italica Millet http://foxtailmillet.genomics.org.cn/page/species/index.jsp
Solanum lycopersicum Tomato http://mips.gsf.de/plant/tomato/download/index.jsp
Solanum tuberosum Potato http://potatogenomics.plantbiology.msu.edu/index.html
Sorghum bicolor Sorghum http://www.phytozome.net/sorghum
Thellugiella parvula Rockface star-violet http://thellungiella.org/
Theobroma cacao Cacao http://cocoagendb.cirad.fr/gbrowse/download.html
Vitis vinifera Grape vine http://www.genoscope.cns.fr/
Volvox carteri Green alga http://www.phytozome.net/dataUsagePolicy.php?org=Org_Vcarteri
Zea mays ssp. mays L. Maize http://www.maizesequence.org/Zea_mays/Info/Index
 
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
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  • 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
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  • 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
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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.
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Contact
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