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Resources (Go to Top)
Plant Genome Databases
TAIR  (http://www.arabidopsis.org/index.jsp)
MaizeGDB (http://www.maizegdb.org/)
Medicago truncatula - A model for legume research (http://www.medicago.org/)
SoyBase and the Soybean Breeder's Toolbox (http://soybase.org/)
Rice genome database (http://rgp.dna.affrc.go.jp/)
GDR|Genome Database for Rosaceae (http://www.rosaceae.org/)
Cucumber genome database (http://cucumber.genomics.org.cn/page/cucumber/index.jsp)
AppleGFDB (http://gfdb.sdau.edu.cn/)
Welcome to the Cacao Genome Project | Cacao Genome Database (http://www.cacaogenomedb.org/)
Brassica oleracea Genomics Database (http://ocri-genomics.org/bolbase/)
BRAD-Brassica Database (http://brassicadb.org/brad/)
Sesamum indicum Genome Database (http://ocri-genomics.org/Sinbase/)
The Banana Genome Hub (http://banana-genome.cirad.fr/home)
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Resource Databases
PlantGDB (http://www.plantgdb.org/)
JGI (http://www.jgi.doe.gov/)
Phytozome (http://www.phytozome.net/)
Entrez Genome Database (http://www.ncbi.nlm.nih.gov/sites/genome)
DOGS-Database Of Genome Sizes (http://www.cbs.dtu.dk/databases/DOGS/)
PGDD - Plant Genome Duplication Database (http://chibba.agtec.uga.edu/duplication/)
MIPS (http://www.helmholtz-muenchen.de/en/ibis)
GRAMENE-Plant Genomic Resources (http://www.gramene.org/)
SGN - Sol Genomics Network (http://www.sgn.cornell.edu/)
Welcome to the Genome Database for Rosaceae | GDR (http://www.rosaceae.org/)
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Comparison of PTGBase and existed tandem-relevant databases (Go to Top)

Database  Contents Species involved Address Authors
STRBase NIST has complied and maintained a Short Tandem Repeat DNA Internet Database since 1997. This database is an information resource for the forensic DNA typing community with details on commonly used short tandem repeat (STR) DNA markers. STRBase collected the abundant literature on this subject to facilitate on-going efforts in DNA typing. Homo sapiens (http://www.cstl.nist.gov/
biotech/strbase)
Ruitberg et al. 2001
Tandem repeats database for bacterial genomes This database ( [http://minisatellites.u-psud.fr] ) collected tandem repeats from publicly available bacterial genomes which facilitates the identification and selection of tandem repeats. The author illustrated the use of this database by the characterization of minisatellites from two important human pathogens, Yersinia pestis and Bacillus anthracis.  Yersinia pestis and Bacillus anthracis (http://minisatellites.u-psud.fr) Le Fleche et al. 2001
YHRD YHRD represents 9-locus Y-STR haplotypes for 1705 African-Americans, European-Americans and Hispanics as of October 2001 and supply the U.S. forensic DNA community with a valuable resource for frequencies of complete or incomplete 9-locus Y-STR haplotypes, as well as information about typing protocols and population genetic analyses. Homo sapiens ((http://www.ystr.org/usa/) Kayser et al. 2002
TRbase TRbase collected tandem repeats to gene locations and disease genes of the human genome and also identified both perfect and imperfect repeats of 1–2000 bp unit lengths. The utility of this database has been illustrated by analysing these repeats for their distribution and frequencies across chromosomes and genomic locations and between protein-coding and non-coding regions. The applicability of this database to identify diseases associated with previously uncharacterized tandem repeats is demonstrated. Homo sapiens (http://trbase.ex.ac.uk/) Boby et al. 2005
TRDB TRDB is a public repository of information on tandem repeats in genomic DNA. It contains a variety of tools for repeat analysis, including the Tandem Repeats Finder program, query and filtering capabilities, repeat clustering, polymorphism prediction, PCR primer selection, data visualization and data download in a variety of formats. Homo sapiens (https://tandem.bu.edu/cgi-bin/trdb/trdb.exe.) Gelfand et al. 2007
TassDB TassDB have stored extensive data about alternative splice events at GYNGYN donors and NAGNAG acceptors. These splice events are of subtle nature since they mostly result in the insertion/deletion of a single amino acid or the substitution of one amino acid by two others. TassDB have collected 114,554 tandem splice sites of eight species, 5,209 of which have EST/mRNA evidence for alternative splicing. In addition, human SNPs that affect NAGNAG acceptors are annotated. Homo sapiens, Canis familiaris, Mus musculus, Rattus norvegicus, Gallus gallus, Danio rerio, Drosophila melanogaster and Caenorhabditis elegans (http://helios.informatik.uni-freiburg.de/TassDB/) Hiller et al. 2007
VNTRDB VNTRDB is a resource for helping in the discovery of putatively polymorphic tandem repeat loci and aids with assay design by providing the flanking sequences that can be used in subsequent PCR primer design. Each TR locus was obtained by comparing the sequences between different sets of bacterial genera, species or strains. Through comparison, TRs which are unique to a genus can also be identified. Moreover, a visualization tool is provided to ensure that the copy number and locus length of repeats are correct. Microorganisms (http://vntr.csie.ntu.edu.tw/) Chang et al. 2007
PTGBase PTGBase is a public database to collect plant genes generated by tandem duplication mechanism in the process of plant evolution. So far, PTGBase mainly focus on plants with available whole genome sequences especially for assembled pseudomolecules with ordered gene models. In this database, we have collected 39 plant species arrayed in 54,130 tandem repeat gene clusters containing 129,652 genes. Plants (http://ocri-genomics.org/PTGBase) Yu et al. 2014
 
References (Go to Top)

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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