DNA Molecular Design Tools

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

Gene Analysis Tools

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

Sanger Sequencing Tool

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

DNA/RNA + Protein Translation

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

Property Calculator (DNA + Protein)

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

Antibody Sequencing

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

Databases and other resources

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


DNA targeting specificity of RNA-guided Cas9 nucleases.

Liu, et al. CRISPR-ERA: a comprehensive design tool for CRISPR-mediated gene editing, repression and activation. Bioinformatics. 31(22):3676–3678 (2015).

Park J., Kim J.-S., and Bae S. Cas-Database: Web-based genome-wide guide RNA library design for gene knockout screens using CRISPR-Cas9. Bioinformatics 32, 2017-2023 (2016).

Rauscher, B.*, Heigwer, F.*, Breinig, M., Winter, J., & Boutros, M. (2016). GenomeCRISPR – a database for high-throughput CRISPR/Cas9 screens. Nucleic Acids Research.

Efficient codon optimization with motif engineering.

Andreas Untergasser, Harm Nijveen, Xiangyu Rao, Ton Bisseling, René Geurts, and Jack A.M. Leunissen: Primer3Plus, an enhanced web interface to Primer3 Nucleic Acids Research 2007 35: W71-W74; doi:10.1093/nar/gkm306.

Ye J, Coulouris G, Zaretskaya I, Cutcutache I, Rozen S, Madden T (2012). Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction. BMC Bioinformatics. 13:134.

AmiRNA Designer – new method of artificial miRNA design.

ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter. Jackman SD, Vandervalk BP, Mohamadi H, Chu J, Yeo S, Hammond SA, Jahesh G, Khan H, Coombe L, Warren RL, Birol I. Genome Research, 2017 27: 768-777.

Integrating long-range connectivity information into de Bruijn graphs; Turner I, Garimella K, Iqbal Z, McVean G (Bioinformatics; Advanced access 15 March 2018).

Hall TA (1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT.Nucl. Acids. Symp. Ser. 41:95-98.

Huang, X. and Madan, A. (1999) CAP3: A DNA sequence assembly program. Genome Res., 9, 868-877.

Warren RL, Sutton GG, Jones SJM, Holt RA. 2007 (epub 2006 Dec 8). Assembling millions of short DNA sequences using SSAKE. Bioinformatics 23:500.

A.L. Delcher, K.A. Bratke, E.C. Powers, and S.L. Salzberg. Identifying bacterial genes and endosymbiont DNA with Glimmer, Bioinformatics 23:6 (2007), 673-679.

Xiaoli Dong, Paul Stothard, Ian J. Forsythe, and David S. Wishart “PlasMapper: a web server for drawing and auto-annotating plasmid maps” Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W660-4.

R. D. Finn, J. Clements, S. R. Eddy. Nucleic Acids Research, 39:W29-37, 2011.

Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data. Carver T, Harris SR, Berriman M, Parkhill J and McQuillan JA. Bioinformatics (Oxford, England) 2012;28;4;464-9. PUBMED: 22199388; PMC: 3278759; DOI: 10.1093/bioinformatics/btr703.

Ying Huang, Beifang Niu, Ying Gao, Limin Fu and Weizhong Li. CD-HIT Suite: a web server for clustering and comparing biological sequences. Bioinformatics, (2010). 26:68.

Fastx-toolkit. FASTQ/A short-reads preprocessing tools (Unpublished).

T-Coffee: A novel method for multiple sequence alignments Notredame, Higgins, Heringa, JMB, 302 (205-217) 2000.

The Pfam protein families database: towards a more sustainable future: R.D. Finn, P. Coggill, R.Y. Eberhardt, S.R. Eddy, J. Mistry, A.L. Mitchell, S.C. Potter, M. Punta, M. Qureshi, A. Sangrador-Vegas, G.A. Salazar, J. Tate, A. Bateman.

CATH: an expanded resource to predict protein function through structure and sequence. Dawson NL, Lewis TE, Das S, Lees JG, Lee D, Ashford P, Orengo CA, Sillitoe I. Nucleic Acids Res. 2017 Jan. doi: 10.1093/nar/gkw1098
Gene3D: Extensive prediction of globular domains in proteins. Lewis TE, Sillitoe I, Dawson N, Lam SD, Clarke T, Orengo CA, Lees JG. Nucleic Acids Res. 2018 Jan. doi: 10.1093/nar/gkx1069.

Waterhouse, A., Bertoni, M., Bienert, S., Studer, G., Tauriello, G., Gumienny, R., Heer, F.T., de Beer, T.A.P., Rempfer, C., Bordoli, L., Lepore, R., Schwede, T. SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res. 46(W1), W296-W303 (2018).