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◆ Research Related Tools

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

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・Blast (Basic Local Alignment Search Tool)

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・NCBI (National Center for Biotechnology Information)

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2. Experimental and Analytical Tools for Molecular Biology.

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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

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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-BLAST: NCBI 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

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〇 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

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〇 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

    ・TIDE : RAPID AND EASY QUANTITATIVE ASSESSMENT OF GENOME EDITING

    ・CRISPR-Cas9 guide RNA design checker from BROAD Institute

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3. Databse

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

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・ Chrysanthemum Genome Database

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・ OrchidBase: comprehensive collection of Orchidaceae floral transcriptomes

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・ TomExpress: Visualize and analyse tomato RNA-seq data

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・ TomGEM: heat tolerance tomato project

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4. Metabolites, Chemicals, and Metabolic networks.

 

・ PUBCHEM

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・ PMN (Plant Metabolic Network)

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・ BIOVIA Software - Freeware

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・ massbank

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

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

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5. Statistical Analysis

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・Jamovi

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・R

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・R studio

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6. 3D Modelling Tools

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・ Avogadro - Free cross-platform molecular editor - Avogadro

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・ Ascalaph Designer - molecular dynamics in graphic environment

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・ Illustrate: Non-photorealistic Biomolecular Illustration

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・ UCSF Chimera: an Extensible  Molecular Modeling System

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・ [PyMOL] Draw Goodsell-like view using GLSL 

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・ PyMOL Wiki!

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・ openmolecules

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・Alphafold

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7. TOOLBOX

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・Early Career Researcher Toolbox: Free Online Molecular Biology Tools

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・Biopython

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・ VANTED - Visualization and Analysis of Networks containing Experimental Data

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・ GeoDa:　An Introduction to Spatial Data Science

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

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・Eurofins Japan: 

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