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Tomato genomic resources database: an integrated repository of useful tomato genomic information for basic and applied research

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Title Tomato genomic resources database: an integrated repository of useful tomato genomic information for basic and applied research
 
Creator Suresh, B. Venkata
Roy, Riti
Sahu, Kamlesh
Misra, Gopal
Chattopadhyay, Debasis
 
Subject Tomato Genomic Resources Database
Tomato
Database
 
Description Accepted date: December 7, 2013
Tomato Genomic Resources Database (TGRD) allows interactive browsing of tomato genes, micro RNAs, simple sequence repeats (SSRs), important quantitative trait loci and Tomato-EXPEN 2000 genetic map altogether or separately along twelve chromosomes of tomato in a single window. The database is created using sequence of the cultivar Heinz 1706. High quality single nucleotide polymorphic (SNP) sites between the genes of Heinz 1706 and the wild tomato S. pimpinellifolium LA1589 are also included. Genes are classified into different families. 5'-upstream sequences (5'-US) of all the genes and their tissue-specific expression profiles are provided. Sequences of the microRNA loci and their putative target genes are catalogued. Genes and 5'-US show presence of SSRs and SNPs. SSRs located in the genomic, genic and 5'-US can be analysed separately for the presence of any particular motif. Primer sequences for all the SSRs and flanking sequences for all the genic SNPs have been provided. TGRD is a user-friendly web-accessible relational database and uses CMAP viewer for graphical scanning of all the features. Integration and graphical presentation of important genomic information will facilitate better and easier use of tomato genome. TGRD can be accessed as an open source repository at http://59.163.192.91/tomato2/.
This work was financially supported by the core grant of National Institute of Plant Genome Research, New Delhi, India and the Department of Biotechnology, Government of India. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
 
Date 2015-12-29T10:28:30Z
2015-12-29T10:28:30Z
2014
 
Type Article
 
Identifier PLoS One, 9(1): e86387
1932-6203
http://172.16.0.77:8080/jspui/handle/123456789/468
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0086387
10.1371/journal.pone.0086387
 
Language en_US
 
Publisher PLOS