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 | 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 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 | 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 Tool
Tools | Description | Resource Link |
---|---|---|
Sanger Sequencing | OMIC Sanger Sequencing: Supplies different types of tools related to Sanger Sequencing | OMIC Sanger Sequencing |
DNA/RNA + Protein Translation
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)
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 Sequencing
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 resources
Databases and other resources
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 |
Other Resources | EOS: Offered popular tools for BioLinux | EOS |
References
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).