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Related Concept Videos

RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
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.

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Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics
08:09

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

Published on: June 17, 2012

Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics.

Hiroaki Sakai1, Sung Shin Lee, Tsuyoshi Tanaka

  • 1Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan.

Plant & Cell Physiology
|January 10, 2013
PubMed
Summary

The updated Rice Annotation Project Database (RAP-DB) now offers comprehensive gene annotations for the rice genome. It includes manually curated data and a new browser for visualizing genetic variations and gene families across plant species.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Plant Science

Background:

  • The Rice Annotation Project Database (RAP-DB) has been a key resource for rice (Oryza sativa) gene annotations since 2005.
  • Previous versions were tied to earlier genome assemblies, necessitating updates for current research.

Purpose of the Study:

  • To present the latest version of RAP-DB, built upon the most recent rice genome assembly (IRGSP-1.0).
  • To enhance the reliability and accessibility of rice gene annotations for researchers.
  • To introduce novel tools for visualizing genetic data and exploring gene relationships.

Main Methods:

  • Mapped transcript and protein sequences from 150 monocot species to identify 37,869 loci.
  • Incorporated literature-based, manually curated data for 1,626 loci.
  • Utilized RNA-Seq and Illumina reads for nucleotide-level transcriptional activity mapping.
  • Developed the Short-Read Assembly Browser (S-RAB) for visualizing alignments, SNPs, and annotations.
  • Created satellite databases (PGFD, IDCGP) for gene family and phylogenetic analyses.

Main Results:

  • The new RAP-DB is based on the IRGSP-1.0 genome assembly.
  • 37,869 loci were identified.
  • 1,626 loci feature literature-based annotations.
  • RNA-Seq data visualizes transcriptional activity at the nucleotide level.
  • S-RAB enables visualization of sequence alignments and single nucleotide polymorphisms (SNPs).
  • PGFD and IDCGP provide insights into gene families and homologous relationships.

Conclusions:

  • The updated RAP-DB provides a highly reliable and up-to-date resource for rice gene annotations.
  • New tools like S-RAB and the satellite databases enhance data accessibility and facilitate comparative genomics.
  • These resources will significantly aid plant and genome researchers in various studies.