ANNOTATE RICE

Rice Genome Annotation Project

Feb 6, 2013 - A paper describing the unified Os-Nipponbare-Reference-IRGSP- 1.0 pseudomolecules and MSU Rice Genome Annotation Project Release 7 has  ...

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The TIGR Rice Genome Annotation Resource: improvements and ...

1 Dec 2006 ... In The Institute for Genomic Research Rice Genome Annotation project (http://rice .tigr.org), we have continued to update the rice genome ...

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pd.rice - Bioconductor

DOI: 10.18129/B9.bioc.pd.rice. Platform Design Info for The Manufacturer's Name Rice. Bioconductor version: Release (3.10). Platform Design Info for The ...

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Rice-Map: a new-generation rice genome browser

30 Mar 2011 ... The Rice Genome Annotation Project at Michigan State University (MSU) has developed a genome browser based on GBrowse system [13], ...

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Indica rice genome assembly, annotation and mining of blast ...

16 Mar 2019 ... We assembled over 86 % (389 Mb) of rice genome and annotated 56,284 protein -coding genes from HR-12 genome using Illumina and ...

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RiceDB: A Web-Based Integrated Database for Annotating Rice ...

RiceDB, a web-based integrated database to annotate rice microarray in various biological contexts was developed. It is composed of eight modules. RiceMap ...

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OryGenesDB Data

13 Nov 2012 ... The 12 rice pseudomolecule sequences are now common to both the MSU Rice Genome Annotation Project and the Rice Annotation Project ...

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RiceChip Annotation Site

3 Mar 2019 ... RGP Rice Genome Project RAP-DB Rice Annotation Project ID Converter converts TIGR & IRGSP loci RiceXPro expression database.

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Transposable element annotation of the rice genome ...

Abstract. Motivation: The high content of repetitive sequences in the genomes of many higher eukaryotes renders the task of annotating them computationally int.

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CARMO: a comprehensive annotation platform for functional ...

A recent report in rice found that the otholog of DOMAINS rearranged ...

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Gene Coexpression Network Analysis as a Source of Functional ...

22 Jul 2011 ... For the purpose of providing functional annotation to rice genes, we found that gene modules identified by coexpression analysis of ...

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RiceDB: A Web-Based Integrated Database for Annotating Rice ...

PDF | RiceDB, a web-based integrated database to annotate rice microarray in various biological contexts was developed. It is composed of eight modules.

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Annotating rice affymetrix data from different gse through biomart

... Column Description labelDescription experimentData: use 'experimentData( object)' pubMedIds: 16183841 Annotation: GPL2025 ## get data from biomaRt ...

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(PDF) The TIGR Rice Genome Annotation Resource: improvements ...

In The Institute for Genomic Research Rice Genome Annotation project (http://rice .tigr.org), we have continued to update the rice genome sequence with new ...

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Gene Ontology annotation of the rice blast fungus, Magnaporthe ...

19 Feb 2009 ... Magnaporthe oryzae, the causal agent of blast disease of rice, is the most destructive disease of rice worldwide. The genome of this fungal ...

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Identification and molecular characterization of tissue-preferred rice ...

27 Nov 2014 ... In rice, the whole genome sequences of both indica and japonica subspecies had been reported [1],[2] and their gene annotation systems are ...

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Full-length transcript-based proteogenomics of rice improves its ...

19 Dec 2019 ... Full-length transcript-based proteogenomics of rice improves its genome and proteome annotation. Mo-Xian Chen, Fu-Yuan Zhu, Bei Gao, ...

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SNP Annotation - Comprehensive Annotation of Rice Multi-Omics

Comprehensive Annotation of Rice Multi-Omics. ... Introduction · Functional Annotation; Transcriptome Analysis. Pair-wise Comparison · Multiple Comparison.

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Annotation of rice contigs

How can I go about annotating contigs of a rice genome? Can I simply do a BLAST search, considering that japonica rice is already annotated? Please give  ...

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Over 1000 rice proteins annotated</span>

3 Oct 2006 ... Headlines. Over 1,000 rice proteins annotated. Rice (Oryza sativa) is the most important food crop in the world and part of the daily diet of over ...

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The Rice Annotation Project Database (RAP-DB): 2008 update ...

17 Dec 2007 ... The Rice Annotation Project Database (RAP-DB) was created to provide the genome sequence assembly of the International Rice Genome ...

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Functional Annotation - Rice Genome Annotation Project

Functional Annotation. May 23, 2007. Rama Maiti. TIGR Rice Workshop. Functional Annotation Overview. • What is annotation. • Steps we take to annotate  ...

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Comparison of rice and Arabidopsis annotation

Comparison of rice and Arabidopsis annotation. Heiko Schoof. Ã and Wojciech M Karlowski y. Several versions of the rice genome were published in 2002,.

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Details - Oryza sativa Indica Group - Ensembl Genomes 46

Oryza sativa Indica Group Assembly and Gene Annotation ... most commonly cultivated sub-species of rice (along with O. sativa Japonica) and is the most widely ...

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Structural variants in 3000 rice genomes

16 Apr 2019 ... Across the rice genomes, we identified regions of high SV frequency ... the general distribution of TEs annotated in the rice reference genome.

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RiceGAAS - omicX

A rice genome automated annotation system. RiceGAAS has the following functional features: (i) collection of rice genome sequences from GenBank; ...

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Retrotranspositional landscape of Asian rice revealed by 3000 ...

3 Jan 2019 ... The recent release of genomic sequences for 3000 rice varieties ... map-based genome assembly, from which TEs have been annotated and ...

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Comparative Genomic Analysis of Rice with Contrasting ...

25 Jul 2019 ... SnpEff was used to annotate SNPs and InDels [36], ... We used a web-based platform, Comprehensive Annotation of Rice Multi-Omics ...

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The Rice Annotation Project Database (RAP-DB): 2008 update*

17 Dec 2007 ... ABSTRACT. The Rice Annotation Project Database (RAP-DB) was created to provide the genome sequence assembly of the International Rice ...

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Annotation of genomic sequences An example on 1 region of the ...

rice chromosome 1. Comparison of automatic annotations obtained with different tools leaves sometimes appear to differences in the number of predicted genes ...

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Improvements to the rice genome annotation through large-scale ...

12 Apr 2019 ... Rice (Oryza sativa) is one of the most important worldwide crops. The genome has ... Track Hubs, to support re-annotation of the rice genome.

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Annotation of the rice genome

A high-quality finished sequence of the rice genome was completed in 2005. However, to maximally use the sequences, quality annotation of the genes and.

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Improvements to the Rice Genome Annotation Through Large-Scale ...

6 Oct 2019 ... Our results can be displayed as tracks on the Ensembl genome or other browsers supporting Track Hubs, to support re-annotation of the rice ...

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Oryza sativa Genome DB

Rice Genome ... Annotated gene models are Release 7. ... Help annotate the Oryza sativa (ssp. japonica) genome using our yrGATE gene structure annotation  ...

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OryzaExpress

22 Apr 2014 ... The integrated database "OryzaExpress" provides information of gene expression network and biological annotations in rice. Rice Gene ...

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Annotate Tab | GenSAS v6.0

Here is an example of a manual curation of a gene model in chromosome 1 of rice. In Figure 50, you will see the JBrowse window at the "Annotate" step.

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Gene Annotation in Rice Genome Using Homology

I created a program and collected cross-referenced database for the rice genome . This program utilizes sequence similarity as a way to annotate all genes with ...

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Nanopore sequencing-based genome assembly and evolutionary ...

5 Feb 2020 ... We examined coding sequences of our circum-basmati genomes by conducting gene annotation using published rice gene models and the ...

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Oryza sativa Kitaake rice

Kitaake, a Japonica rice variety, is neutral to photoperiod changes and has a very ... from multiple rice tissues were used in the genome annotation as described ...

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Extensive sequence divergence between the reference genomes of ...

17 Aug 2019 ... Here, we generated high-quality genome sequences for two elite rice ... annotation and analysis of the two genomes and transcriptomes.

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