Bioinformatics Tool



DNA Molecular Design ToolsGene Analysis ToolsSanger Sequencing Tool
DNA Molecular Design ToolsGene Analysis ToolsSanger Sequencing Tool
DNARNA + Protein TranslationProperty Calculator (DNA + Protein)Antibody Sequencing
DNA/RNA + Protein TranslationProperty Calculator
(DNA + Protein)
Antibody Sequencing
Databases and other resources
Databases and other resources


 
DNA Molecular Design Tools

Gene EditingMIT: Input sequence and can discover possible off targets genome-wide + highlighting guides with high target specificityView
Gene Editing Services
CRISPR-ERA: a comprehensive design tool for CRISPR-mediated gene editing, repression and activationView
Gene Editing Services
Cas-Database: web-based genome-wide guide RNA library design for gene knockout screens using CRISPR-Cas9View
Gene Editing Services
GenomeCRISPR: a database for high-throughput CRISPR/Cas9 screensView
Gene Editing Services
Codon OptimizationCodon Optimizer: Remove/add motifs + codon optimizationView
NGTM Codon
PCR Primer DesignPrimer3Plus: Picks primers from a DNA sequenceView
Primer-Blast: Tool for finding primers specific to PCR templateView
Molecular DesignMolecular Design ToolKit: Requires python, able to design and visualize interaction in molecular systemsView
AmiRNA: Design artificial micro RNAs based on data provided by userView


 
Gene Analysis Tools

Sequencing and Genomic Assemblers Abyss: de novo, parallel, pair-end sequence assembler designed for short reads, show what sequence will becomeView
Cufflinks: Assembles transcripts, estimates abundances, tests for differential expression and regulation in RNA-Seq samplesView
Cortex Con: de novo gene assembly, multisample variant calling, manipulating and assembling graphsView
BioEdit: Sequence Aligner, plasmid drawing, multiple analysis toolsView
CAP3: Sequence Assembly Program (Contigs, Single Sequence)Website
Download
SSAKE: de novo genome assembly with short DNA sequence readsView
FALCON: Allows alignment of long reads for consensus and assemblyView
Gene Sequence AnalysisGLIMMER: Identify areas of coding vs. non-coding in microbial DNAView
EMBOSS Seqret: Reads/Writes sequences (Extract sequences from database, display/reformat sequence, FASTA file converter, reverse complement, sequence case conversion)View
User Guide
PlasMapper: Generates and annotates plasmid maps with given plasmid sequenceView
Plasmid Prep Services
HMMER: Searching databases for sequence homologs + alignmentsView
Online Tool
User Guide
Artemis: Visualization of sequence features, next generation dataView
BLAST: Genome database + sequence alignment toolView
CD-Hit: Clustering/comparing nucleotide or protein sequencesView
FASTX-TOOLKIT: Preprocess fastx/q files to produce better mapping (alignment) results to reference other genomes/databasesView
Bioperl: Sequence Alignment, manipulating sequences, transforming formats, accessing data from databasesView
CLUSTALW: Multiple Sequence AlignmentView
T-COFFEE: Align DNA, RNA, or Protein SequencesView
Reverse Complement: Outputs the reverse complement sequenceView


 
Sanger Sequencing Tool

Sanger SequencingOMIC Sanger Sequencing: Supplies different types of tools related to Sanger SequencingView
Sanger Sequencing Services

 

DNA/RNA + Protein Translation

DNA/RNA – ProteinExPASy: Translates DNA/RNA sequence to protein sequenceView
Protein – DNASequence Manipulation Suite: Reverse translationView


 
Property Calculator (DNA + Protein)

Property CalculatorDNA + Protein Calculator: Properties of DNA + ProteinProtein
DNA
Protein Structure + Function Pfam: Finds protein alignment/matches, domain organization + functionView
PROSITE: Protein domains, functional sites, associated patternsView
CATH: Classifications of proteins downloaded from PDB, predict locations of structural domains, structure, function and evolution of proteinsView
SWISS-MODEL: Protein structure homology modelling serverView


 
Antibody Sequencing

Antibody SequencingIgblast: A tool for immunoglobulin (IG) and T cell receptor (TR) V domain sequencesView
Antibody Services
IMGT: the international ImMunoGeneTics information systemView
Antibody Services


 
Databases and other resources

DatabasesSanger Institute: Provides many different tools for genome analysisView
Protein Data Bank: Provides numerous information related to proteinsView
NCBI: Genome DatabaseView
OMIC Tools: Provides selection of bioinformatics toolsView
Other ResourcesElements of Genomics: Offers numerous popular bioinformatic toolsView
Researchgate: Article offering insight on tools for gene and protein sequence analysisView
EOS: Offered popular tools for BioLinuxView

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).