Bioinformatics Tool

DNA Molecular Design Tools

Gene Analysis Tools

Sanger Sequencing Tool

DNA/RNA + Protein Translation

Property Calculator (DNA + Protein)

Antibody Sequencing

Databases and other resources

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).