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Related Concept Videos

Genome Annotation and Assembly03:36

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
Genomics02:02

Genomics

Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...

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Tomato Functional Genomics Database: a comprehensive resource and analysis package for tomato functional genomics.

Zhangjun Fei1, Je-Gun Joung, Xuemei Tang

  • 1Boyce Thompson Institute for Plant Research, Cornell University, USDA Robert W Holley Center for Agriculture and Health, Ithaca, NY 14853, USA. zf25@cornell.edu

Nucleic Acids Research
|October 23, 2010
PubMed
Summary

The Tomato Functional Genomics Database (TFGD) now integrates gene expression, metabolite, and small RNA (sRNA) data for comprehensive tomato research. This resource enables advanced data mining and analysis for improved tomato functional genomics discovery.

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Area of Science:

  • Plant biology
  • Genomics
  • Bioinformatics

Background:

  • Functional genomics generates large datasets requiring integrated storage and analysis.
  • Previous resources like the Tomato Expression Database lacked comprehensive data integration.
  • The need for advanced tools to mine and analyze complex tomato genomic data.

Purpose of the Study:

  • To develop and present the expanded Tomato Functional Genomics Database (TFGD).
  • To integrate diverse functional genomics data, including gene expression, metabolite profiles, and small RNA (sRNA) data.
  • To provide advanced query and analysis tools for intelligent data mining.

Main Methods:

  • Development of computational pipelines for processing microarray, metabolite, and sRNA data.
  • Integration of diverse datasets within a centralized database architecture.
  • Implementation of query interfaces and analysis tools for gene co-expression, pathway analysis, and miRNA target identification.

Main Results:

  • TFGD successfully integrates large-scale tomato functional genomics datasets.
  • Developed pipelines enable efficient processing and analysis of diverse data types.
  • Provided tools facilitate the identification of co-expressed genes, biological pathways, and miRNA targets.
  • Enabled integration of transcriptomic and metabolomic profiles, and sRNA and mRNA sequences.

Conclusions:

  • TFGD serves as a comprehensive, integrated resource for tomato functional genomics.
  • The database and its associated tools facilitate advanced data mining and biological discovery.
  • TFGD supports researchers in exploring complex interactions within tomato functional genomics data.