Synthetic Biology:Tools

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Synthetic Biology is
A) the design and construction of new biological parts, devices, and systems, and
B) the re-design of existing, natural biological systems for useful purposes.

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This page contains a collection of links to online tools that are related to Synthetic Biology. <wikionly>If you are editing this page, please try to keep the tools in alphabetical order, by tool name.</wikionly>

DNA Tools

• BBOCUS by Ferro and Purrello lab
  • BBOCUS (BackTranslation Based On Codon Usage Strategy) is a re-implementation of the algorithm in Graziano Pesole's BACKTR. It's based on cluster analysis (Complete Linkage algorithm), that requires a similarity matrix D containing distance between each pair of sequences of mRNA. After cluster analysis, backtranslation is performed on sequences of homogeneous pool. Unlike in Graziano Pesole's method, where the choose of homogeneous pool was made by a biologist, the choose of cluster in BBOCUS is fully automatic. A Codon Usage Table (CUT) is created through sequences of homogeneuos pool. Generally, to backtranslate an amino acid in a protein the codon chosen it is the one has maximum frequency.

• Biopolymer calculator by Schepartz lab
  • Calculate extinction coefficients, Tm's, and base composition for your DNA or RNA; calculate amino acid composition and extinction coefficient for your protein

• Clipboard by Austin Che
  • Web tool for getting complement, reverse complement, translation and restriction enzyme analysis of a DNA sequence

• DNAWorks by Hoover and Lubkowski
  • A web tool for optimizing melting temperature during gene synthesis.

• File format converter by Austin Che
  • Web tool for converting between sequence file formats.

• Genome Compiler by Genome Compiler
  • Genome Compiler is the industry's most user friendly genetic engineering design tool. It allows you to manipulate genetic information; from genes to plasmids to whole genomes. You can rapidly access extensive libraries of genetic parts, and easily order your final design from a variety of providers.
  • Some of the key features include: a user-friendly workspace for handling genetic constructs of all sizes, a powerful gene search capability with lightning fast NCBI access, a built-in constructs library that includes a parts registry, vectors-plasmids, complete genomes, as well as seamless collaboration through the Genome Compiler Cloud. Additionally you can drag components between layers and projects (in multiple tabs), design genetic constructs across tightly integrated layers; operon/part level, amino acid, and DNA, perform re-annotation and reverse complement, employ automatic sequence detection to point out restriction enzymes and protein sub-domains.

• GeneDesign by Boeke lab
  • Collection of online (and some command line) tools for codon optimization and shuffling, restriction site editing, and so on.

• GeneDesigner by DNA2.0
  • Combine genetic building blocks by drag-and-drop, codon optimize, restriction site editing, sequence oligo design etc. See BMC Bioinformatics 2006 Jun 6;7(1):285 for more detail.
  • Free to download and works on Mac or PC. User agreement is somewhat restrictive (i.e., does not allow you to sell genes designed on the program without permission).

• GenoCAD
  • An experimental site that relies on formal grammars to design and verify the synthetic DNA sequences.
  • The theoretical foundations of GenoCAD were published in Bioinformatics.

• NEB Cutter by New England Biolabs, Inc.
  • Tool for finding restriction sites, et cetera.

• Synthetic Gene Designer by Gang Wu
  • A web platform that allows codon optimization to various extent.
  • Compatible with non-standard genetic codes
  • Integrate CUTG
  • Restriction site avoidance
  • Oligo design

• Vector NTI by Informax, Inc.
  • Free-to-academics tool for sequence analysis and data management.

• j5, DeviceEditor, and VectorEditor online tools
  • j5: DNA assembly design automation for (combinatorial) flanking homology (e.g., SLIC/Gibson/CPEC/SLiCE/yeast) and type IIs-mediated (e.g., Golden Gate/FX cloning) assembly methods
  • DeviceEditor: a visual DNA design canvas that serves as front-end for j5
  • VectorEditor: a visual DNA editing and annotation tool
  • The j5 and DeviceEditor software has been exclusively licensed to TeselaGen Biotechnologies for commercial use and distribution.

RNA Tools

• Appendix by Ambion, Inc.
  • Website with many useful nucleic acid parameters.

• mFold by Michael Zuker.
  • This is the main page with links to sites for predicting RNA and DNA folds, calculating Tm's and free energies.

Protein Tools

• Cn3D by NCBI
  • A helper application for your web browser that allows you to view 3-dimensional structures from NCBI's Entrez retrieval service. It doesn't read PDB files but can be more straightforward to use than DeepView.

• DeepView by GlaxoSmithKline & Swiss Institute of Bioinformatics
  • Awesome program for viewing and studying protein structure.

• ExPASy Proteomics server by the Swiss Institute of Bioinformatics
  • Collection of links to many pages to calculate parameters of your favorite proteins

• Modeller by Sali Lab
  • For homology or comparative modeling of protein three-dimensional structures.

• Zinc Finger Tools by Barbas Lab
  • Design Zinc Finger DNA binding proteins

CAD Tools

• TinkerCell by Deepak Chandran
  • Construct computational models using biological parts, cells, and modules
  • Plug-in interface allows contributors to add new features and functions (C and Python)
  • Designed to bridge computational and experimental biology

• Metabolic Tinker by Kent McClymont and Orkun Soyer
  • Construct thermodynamically feasible metabolic paths among user-defined compounds
  • Developed on all available metabolic data (updated regularly)
  • Source code available for further development

General Tools

• Colibri by Institut Pasteur
  • E. coli genome site; get sequences, see the position of your gene in the chromosome, see the function of your gene, and other fun stuff. You can also search for protein sequences/motifs within the E. coli genome.

• Registry of Standard Biological Parts by MIT
  • Open repository of BioBricks; the place for all your standard biological parts.

• The public instance of the JBEI Registry
  • A DNA part, plasmid, microbial strain, and Arabidopsis Seed online repository with physical sample tracking capabilities
  • A site where you can explore the various features of the JBEI Registry software, and even get some work done!
  • Try out the integrated online tools, including DNA sequence editing and annotation (Vector Editor) and auto-aligning sequencing trace files against a template.
  • Follow a link to the underlying open-source software source code.

• PaR-PaR Laboratory Automation Platform
  • PaR-PaR allows researchers to use liquid-handling robots effectively, enabling experiments that would not have been considered previously. After minimal training, a biologist can independently write complicated protocols for a robot within an hour.

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