Useful Links

Databases
Genome Projects
- Rice | Arabidopsis thaliana | Agriculture/ Plant | Other
Research Information
- Rice | Assorted Collection | Documentation
Bioinformatics Tools
- Annotation tools | Comparison Search | Genome Research
Rice Chromosome 5 Related
- Marker | Genetic Map
Mutant Research

Databases

DDBJ in National Institute of Genetics, Japan

EMBL : WWW services , SRS , BioCatalog , in EMBO , Europe

NCBI : Entrez , BLAST in NLM, NIH, U.S.

NHRI: HINT , mirror site of ExPasy, GDB

SWISS-PORT

PIR : Protein information resources , protein sequences database PIR-PSD, protein classification database iProClass

PDB : mirror sit in Taiwan

Database Categories List of NAR journal

Databases by Dept of Plant Gene Research, Kazusa DNA Research Institute

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Genome Projects

[ Rice | Arabidopsis thaliana | Agriculture/ Plant | Other ]

Rice

Genome project

RGP in STAFF, Japan

Rice BAC End Sequencing Project in Clemson U.Genomics Institute

The TIGR Rice Genome Project

Rice Genome Analysis in Cold Spring Harbor Laboratory

The Plant Genome Initiative at Rutgers (PGIR)

National Center for Gene Research in Chinese Academy of Science

Rice Genome of Korea

IRD center of Montpellier, France

International Rice Research Institute (IRRI)

Rice insertion mutant database (Experimental)

Rice Microarray Opening Site (RMOS)

University of Wisconsin Madison Rice Genome Project

Genoscope

Gene Discovery by Functional Genomics

Other effort

Rice GD

Monsanto rice-research.org

Syngenta

Torrey Mesa research institute

Rice sequence information

TIGR Rice Gene Index (OsGI)

TIGR rice repeat DNA database

The Korea Rice Genome Database

Rice Sequence Analysis Project by CBC, UMN

The Oryza sativa Transposable Element Database

Rice fingerprinting map by CUGI

Rice GAAS by RGP

TIGR annotation

MAFF RiceDB

Functional genomics

International Rice Research Institute (IRRI)

The Rice Functional Genomics Program (RIFGP), China

Rice Microarray Openning Site, Japan

Maize-Rice Functional Genomics Project (CIMMYT and IRRI)

CAMBIA's TransGenomics Initiative (TGI)

Gramene: A Comparative Mapping Resource for Grains

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Arabidopsis thaliana

TAIR : The Arabidopsis Information Resource

Arabidopsis Functional Genomics Consortium (AFGC) in U. Stanfard

Aims in Michigan U.

NASC in Nottinghan

ATGC in Pennsylvania U.

Arabidopsis thaliana Database in TIGR

KAOS in Kazusa

Arabidopsis thaliana Genome Gene Identification Table

Munich Information Center for Protein Sequencs (MIPS)

Arabidopsis Transposon Insertion Service (ATIS)

Arabidopsis Thaliana Insertion Database (ATIdb)

Arabidopsis Seed EST Project in Michigan State U.

Arabidopsis links by TIGR

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Agriculture/ Plant

Agriculture Genome Information System

Agricultural Databases for Decision Support

MaizeDB in USDA-ARS ( Missouri-Columbia U.)

Plant Genome Databases

Grain Genes at USDA/NAL

Plant Disease Resistance Genes Database (R-Genes)

Medicago Genome Initiative(MGI) by NCGR

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Others

VGH-YMU Human Genome Sequencing Projects in Taiwan

ACGT in U.Oklahoma

GenomeNet in Japan

GDB: The Genome Database

Human Genome Project

TIGR: includes database and software

The Sanger Centre : Human , C. elegans, Database

Maize Targeted Mutagenesis Database (mtmDB)

Medicago truncatula Consortium

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Research Information

[ Rice | Assorted Collection | Documentation ]

Rice

Rice Genes in Cornell

Rice Genetics Research at USDA-ARS

Rice Web in IRRI

Oryzabase gather knowledge from classical rice genetics to recent genomics

BAC-based Physical Map by Texas A&M

Rice-research of Monsanto

Announce of complete rice genome map by Syngenta

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Assorted Collection

Biosis Software

Biology Software by Dr. Mick Partis, also abundant resources and links of biology

BioToolKit in BioSupplyNet, collection for the study of nucleic acid, genome, and protein structure.

CBS (Center for Biological Sequence Analysis), Technical University of Danmark

Database Categories List of NAR journal

Japan Science and Technology Corporation (JST) :YEBIS, GeneWalker

Softwares develpmented by TIGR, like Glimmer, MUMmer, Annotator, Assembler

Weizmann Institute in Israel, useful tools like GeneCards, 3DB Browser

Assembly program Phred/Phrap/Consed System ,Repeatmaskerin genome center in U. Washington

DNA and Protein Analysis Toolkit by U. Rockefeller

NEE-HOW : The Bioresource Finder

European Bioinformatics Institute EBI

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Documentation

A Bibliography on Computational Gene Recognition

GCG : Announcements and information from Oxford Molecular Company

Document at NHRI

POST: Chinese document

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Bioinformatics tools

[ Annotation tools | Comparison Search ]

Annotation tools

Genome Annotation Consortium : Collection of annotation tools , data sources and catalog

Gene Code : Sequencher

GeneMark

Genotator: A Workbench for Sequence Annotation and Browsing

GRAIL at ORNL

Genscan at MIT

RiceGAAS and RiceHMM by RGP

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Comparison Search

NetGene , ChloroP , TMHMM at CBS (Center for Biological Sequence Analysis), Technical U. of Danmark

FLAG(Fast Local Alignment for Gigabases) :developed by BMEC, ITRI, Taiwan

GenomeNet : pathway databaseKEGG , motif search toolMotif , intergrated IDEAS

InterPro : Integrated Resource of Protein Domains and Functional Sites of EBI

Miropeats-Graphical DNA comparisons , by Jeremy Parsons

PSORT : prediction of protein localization sites in cells

SplicePredictor- a method to identify potential splice sites in (plant) pre-mRNA by sequence inspection

Sean Eddy's lab in Washington U. -- searchong tools with HMM : HMMER ,PFAM, tRNAscan-SE

The Baylor College of Medicine Search Launcher

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Genome Research

Ensembl Genome Server

GenomeWeb - Lists of Genome Sites by UK Human Genome Mapping Project Resource Centre

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Rice Chromosome 5 Related

Marker

A High-Density Rice Genetic Map

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Mutant Research

Rice insertional mutants database

TRIM: Taiwan Rice Insertional Mutants Database

TOS17

Rice traditional mutant database

IRRI-IR64 mutant database

Oryzabase

Arabidopsis insertional mutant database

Arabidopsis insertional database

Arabidopsis Transposon Insertion Service (ATIS)

Cold Spring Harbor Arabidopsis Genetrap Website

Description of the GARLIC Project at TMRI

Other plant mutants database

Maize Targeted Mutagenesis Database

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