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Bioinformatics Tools
Home > Bioinformatics Tools > Bioinformatics Tools
DNA Molecular Design ToolsView More

    Tools Description Resource Link
    Gene Editing MIT: Input sequence and can discover possible off targets genome-wide + highlighting guides with high target specificity Guide Design Zhang Lab
    Gene Editing CRISPR-ERA: a comprehensive design tool for CRISPR-mediated gene editing, repression and activation sgRNA design Stanford
    Gene Editing Cas-Database: web-based genome-wide guide RNA library design for gene knockout screens using CRISPR-Cas9 CRISPR RGEN Tools
    Gene Editing GenomeCRISPR: a database for high-throughput CRISPR/Cas9 screens GenomeCRISPR
    Codon Optimization Codon Optimizer: Remove/add motifs + codon optimization Codon Optimizer
    PCR Primer Design Primer3Plus: Picks primers from a DNA sequence Primer3Plus
    PCR Primer Design Primer-Blast: Tool for finding primers specific to PCR template Primer-Blast
    Molecular Design Molecular Design ToolKit: Requires python, able to design and visualize interaction in molecular systems Molecular Design Toolkit
    Molecular Design AmiRNA: Design artificial micro RNAs based on data provided by user AmiRNA Designer

Gene Analysis ToolsView More

    Tools Description Resource Link
    Sequencing and Genomic Assemblers Abyss: de novo, parallel, pair-end sequence assembler designed for short reads, show what sequence will become ABySS
    Sequencing and Genomic Assemblers Cufflinks: Assembles transcripts, estimates abundances, tests for differential expression and regulation in RNA-Seq samples Cufflinks
    Sequencing and Genomic Assemblers Cortex Con: de novo gene assembly, multisample variant calling, manipulating and assembling graphs McCortex
    Sequencing and Genomic Assemblers BioEdit: Sequence Aligner, plasmid drawing, multiple analysis tools BioEdit
    Sequencing and Genomic Assemblers CAP3: Sequence Assembly Program (Contigs, Single Sequence) CAP3 Sequence Assembly Program
    Sequencing and Genomic Assemblers SSAKE: de novo genome assembly with short DNA sequence reads SSAKE
    Sequencing and Genomic Assemblers FALCON: Allows alignment of long reads for consensus and assembly FALCON
    Gene Sequence Analysis GLIMMER: Identify areas of coding vs. non-coding in microbial DNA GLIMMER
    Gene Sequence Analysis EMBOSS Seqret: Reads/Writes sequences (Extract sequences from database, display/reformat sequence, FASTA file converter, reverse complement, sequence case conversion) EMBOSS Seqret
    Gene Sequence Analysis PlasMapper: Generates and annotates plasmid maps with given plasmid sequence PlasMapper
    Gene Sequence Analysis HMMER: Searching databases for sequence homologs + alignments HMMER
    Gene Sequence Analysis Artemis: Visualization of sequence features, next generation data Artemis
    Gene Sequence Analysis BLAST: Genome database + sequence alignment tool BLAST
    Gene Sequence Analysis CD-Hit: Clustering/comparing nucleotide or protein sequences CD-Hit
    Gene Sequence Analysis FASTX-TOOLKIT: Preprocess fastx/q files to produce better mapping (alignment) results to reference other genomes/databases FASTX-Toolkit
    Gene Sequence Analysis Bioperl: Sequence Alignment, manipulating sequences, transforming formats, accessing data from databases Bioperl
    Gene Sequence Analysis CLUSTALW: Multiple Sequence Alignment CLUSTALW
    Gene Sequence Analysis T-COFFEE: Align DNA, RNA, or Protein Sequences T-COFFEE
    Gene Sequence Analysis Reverse Complement: Outputs the reverse complement sequence Reverse Complement

Sanger Sequencing ToolView More

    Tools Description Resource Link
    Sanger Sequencing OMIC Sanger Sequencing: Supplies different types of tools related to Sanger Sequencing OMIC Sanger Sequencing

DNA/RNA + Protein TranslationView More

    Tools Description Resource Link
    DNA/RNA – Protein ExPASy: Translates DNA/RNA sequence to protein sequence ExPASy
    Protein – DNA Sequence Manipulation Suite: Reverse translation Sequence Manipulation Suite

Property Calculator (DNA + Protein)View More

    Tools Description Resource Link
    Property Calculator DNA + Protein Calculator: Properties of DNA + Protein Property Calculator
    Protein Structure + Function Pfam: Finds protein alignment/matches, domain organization + function Pfam
    Protein Structure + Function PROSITE: Protein domains, functional sites, associated patterns PROSITE
    Protein Structure + Function CATH: Classifications of proteins downloaded from PDB, predict locations of structural domains, structure, function and evolution of proteins CATH
    Protein Structure + Function SWISS-MODEL: Protein structure homology modelling server SWISS-MODEL

Antibody SequencingView More

    Tools Description Resource Link
    Antibody Sequencing Igblast: A tool for immunoglobulin (IG) and T cell receptor (TR) V domain sequences Igblast
    Antibody Sequencing IMGT: the international ImMunoGeneTics information system IMGT

Databases And Other ResourcesView More

    Tools Description Resource Link
    Databases Sanger Institute: Provides many different tools for genome analysis Sanger Institute
    Databases Protein Data Bank: Provides numerous information related to proteins Protein Data Bank
    Databases NCBI: Genome Database Genome Database
    Databases OMIC Tools: Provides selection of bioinformatics tools OMIC Tools
    Other Resources Elements of Genomics: Offers numerous popular bioinformatic tools Elements of Genomics
    Other Resources Researchgate: Article offering insight on tools for gene and protein sequence analysis Researchgate

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