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◆ Research Related Tools

1. Searching for target genes, nucleotide, RNAs, proteins, etc.

Blast (Basic Local Alignment Search Tool)

NCBI (National Center for Biotechnology Information)

2. Experimental and Analytical Tools for Molecular Biology.

〇 Primer設計

 Primer3Plus  プライマー設計

 ・Thermo Scientific Web Tools

      Multiple Primer Analyzer : For analyzing and comparing multiple primer sequences simultaneously.

 ・FastPCR : プライマー設計

 ・Real tim PCR プライマー設計:QPCR ASSAY DESIGN

    Primer-BLAST : A tool for finding specific primers

〇 アライメント

 ・MEGA: Molecular Evolutionary Genetics Analysis

 ・Clustal: Multiple Sequence Alignment :アライメントツール. Clustal Omega is the new version of ClustalW/ClustalX

 ・BioEdit : Biological Sequence Editor, Alignment editor. Windows7 available.

 ・Chromas Lite : DNAシーケンサビューワー.

 ・GeneDoc : アライメントエディタ. 論文用作図.

 ・Gene Studio : Free Molecular Biology Tool, Sequence viewer, Tree Alignment, Tree editing

    Magic-BLASTNCBI Magic-BLAST RNA-seq mapping tool

    UGENE free open-source cross-platform bioinformatics software

    Jalview: a free program for multiple sequence alignment editing, visualisation and analysis

Plasmid Design

 ・ApE A :  plasmid map Editor

 ・Serial Cloner : GUI based plasmid map Editor

    ・SnapGene Viewer: Plasmid map viewer

    ・pDRAW32: Plasmid map viewer

    ・XPlasMap: Plasmid map editor for Mac

形質転換(Gene Transformation)

 ・CRISPRdirect : CRISPR/casのターゲットシーケンスの決定

 ・Choosing the right tool for designing guide RNAs from TaKaRa Bio

    ・CRISPR Guide by addgene

    ・GPP sgRNA Designer from BROAD Institute


    ・CRISPR-Cas9 guide RNA design checker from BROAD Institute

3. Databse

・ Mum GARDEN (Mum Genome And Resource Database ENtry) : キクタニ菊のDNAデータベース

・ Chrysanthemum Genome Database

・ OrchidBase: comprehensive collection of Orchidaceae floral transcriptomes

・ TomExpress: Visualize and analyse tomato RNA-seq data

・ TomGEM: heat tolerance tomato project

4. Metabolites, Chemicals, and Metabolic networks.



・ PMN (Plant Metabolic Network)

・ BIOVIA Software - Freeware

・ massbank

・ Lablicate: Openchrom - an open source software for chromatography, spectrometry and spectroscopy

・ AMDIS: a freely available and sophisticated  software for GC-MS data interpretation from NIST

5. Statistical Analysis



R studio

6. 3D Modelling Tools

 Avogadro - Free cross-platform molecular editor - Avogadro

Ascalaph Designer - molecular dynamics in graphic environment

・ Illustrate: Non-photorealistic Biomolecular Illustration

・ UCSF Chimera: an Extensible  Molecular Modeling System

・ [PyMOL] Draw Goodsell-like view using GLSL 

PyMOL Wiki!

・ openmolecules


Early Career Researcher Toolbox: Free Online Molecular Biology Tools


・ VANTED - Visualization and Analysis of Networks containing Experimental Data

・ GeoDa: An Introduction to Spatial Data Science

・ ProteoWizard: Proteomics analysis made simple. It's like magic.

Eurofins Japan

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