Tag: Rice

PhosphoRice 1.1.1 – Meta-predictor of Rice-specific Phosphorylation Site

PhosphoRice 1.1.1

:: DESCRIPTION

PhosphoRice, a meta-predictor of rice-specific phosphorylation site, was constructed by integrating the newly phosphorylation sites predictors, NetPhos2.0, NetPhosK, Kinasephos, Scansite, Disphos and Predphosphos with parameters selected by restricted grid search and random search

::DEVELOPER

Huaqin He’s Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

 PhosphoRice

:: MORE INFORMATION

Citation

Plant Methods. 2012 Feb 3;8:5. doi: 10.1186/1746-4811-8-5.
PhosphoRice: a meta-predictor of rice-specific phosphorylation sites.
Que S1, Li K, Chen M, Wang Y, Yang Q, Zhang W, Zhang B, Xiong B, He H.

PRIN – Predicted Rice Interactome Network

PRIN

:: DESCRIPTION

PRIN is the first well annotated protein interaction database for the important model plant Oryza sativa. It has greatly extended the current available protein-protein interaction data of rice with a computational approach, which will certainly provide further insights into rice functional genomics and systems biology.

::DEVELOPER

Ming Chen’s Bioinformatics Group, Zhejiang University.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PRIN: a predicted rice interactome network.
Gu H, Zhu P, Jiao Y, Meng Y, Chen M.
BMC Bioinformatics. 2011 May 16;12:161. doi: 10.1186/1471-2105-12-161.

OsCAS – Annotation platform for Rice Microarray data

OsCAS

:: DESCRIPTION

OsCAS (Oryza sativa Chips Annotation System) is a comprehensive system designed to annotate the results of rice microarray experiments and analysis relationships between genes based on their expression. The aim of the platform is to facilitate the study of differently expressed genes in the microarray experiments within the framework of systems biological research.

::DEVELOPER

Ming Chen’s Bioinformatics Group, Zhejiang University.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Qingyun Shi, Yijun Meng, Dijun Chen, Fei He, Haibin Gu, Ping Wu, Ming Chen(2010)
OsCAS: a comprehensive web-based annotation platform for rice microarray data.
BioChip Journal, 4(1): 9-15.

RPAN 0.91 – Rice Pan-genome Browser for 3K rice genomes

RPAN 0.91

:: DESCRIPTION

RPAN is a genome browser to search and visualize the rice pan-genome derived from 3K RGP. RPAN contains a database of the basic information of 3010 rice accessions, including genomic sequences, gene annotations, PAV information and gene expression data of the rice pan-genome. At least 12 000 novel genes absent in the reference genome were included. RPAN also provides multiple search and visualization functions. RPAN can be a rich resource for rice biology and rice breeding.

::DEVELOPER

Dr. Chaochun Wei

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser / Linux with apache server.

:: DOWNLOAD

RPAN

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2017 Jan 25;45(2):597-605. doi: 10.1093/nar/gkw958. Epub 2016 Dec 10.
RPAN: rice pan-genome browser for ～3000 rice genomes.
Sun C et al.

iDNA6mA-Rice – Detecting N6-Methyladenine Sites in Rice

iDNA6mA-Rice

:: DESCRIPTION

iDNA6mA-Rice is a tool for the identification of 6mA (N6-methyladenine) sites in the rice genome.

::DEVELOPER

LinDing Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser / Linux

:: DOWNLOAD

iDNA6mA-Rice

:: MORE INFORMATION

Citation

iDNA6mA-Rice: A Computational Tool for Detecting N6-Methyladenine Sites in Rice.
Lv H, Dao FY, Guan ZX, Zhang D, Tan JX, Zhang Y, Chen W, Lin H.
Front Genet. 2019 Sep 10;10:793. doi: 10.3389/fgene.2019.00793.

CARMO v1.0 – Comprehensive Annotation of Rice Multi-Omics

CARMO v1.0

:: DESCRIPTION

CARMO is a web-based platform providing comprehensive annotations for multi-omics data, including transcriptomic data sets, epi-genomic modification sites, SNPs from genome re-sequencing, and the large gene lists derived from these omics studies.

::DEVELOPER

Plant Bioinformatics and Functional Epigenomics Group, SIPPE, SIBS, CAS

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

CARMO: a comprehensive annotation platform for functional exploration of rice multi-omics data.
Wang J, Qi M, Liu J, Zhang Y.
Plant J. 2015 Jul;83(2):359-74. doi: 10.1111/tpj.12894.

Diurnal 2.0 – Mining and Viewing Diurnal and Circadian Microarray data for Arabidopsis thaliana, poplar, and rice

Diurnal 2.0

:: DESCRIPTION

Diurnal is a web-based tool for accessing the diurnal and circadian genome-wide expression results of genes from several array experiments conducted on common model plants. The expression patterns of particular loci or array probes can be looked up under a variety of different conditions. For each condition, every expression pattern has been modeled using a periodic pattern, which has then been used to estimate the phase of peak expression.

::DEVELOPER

Mockler Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation:

The DIURNAL project: DIURNAL and circadian expression profiling, model-based pattern matching, and promoter analysis.
Mockler TC, Michael TP, Priest HD, Shen R, Sullivan CM, Givan SA, McEntee C, Kay SA, Chory J.
Cold Spring Harb Symp Quant Biol. 2007;72:353-63. doi: 10.1101/sqb.2007.72.006.

cM Converter – Convert in Batch Physical to Genetical Map Positions of Molecular Markers of Rice

cM Converter

:: DESCRIPTION

cM Converter (centimorgan converter) is a program to convert in batch physical to genetical map positions of molecular markers of rice.

::DEVELOPER

Mathias Lorieux

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX
  • Excel

:: DOWNLOAD

 cM Converter

:: MORE INFORMATION