Web Tools for Synthetic Biology

Genetic Parts

• Registry of Standard Biological Parts

  Public registry of standard biological parts; mostly for iGEM.

• SEVA

  Architecture and repository for standard plasmid designs.

• Addgene

  Commercial collection of plasmids.

• SynBERC registry

  Public registry of biological parts; mostly for SynBERC members.

• JBEI registry

  Public registry of standard biological parts.

• BioFab

  Collection of promoters, BCDs and terminators characterized by Drew Endy's Lab

• FPbase

  Database for fluorescent protein references, data and comparison tools.

Sequence Design

• Salis Lab software tools

  Multiple tools for sequence design of non repetitive parts, encompassing the RBS calculator, RBS Library calculator, Operon Calculator, ELSA (CRISPR array) calculator, Non-Repetitive Parts calculator and a Riboswitch calculator.

• RBS Calculator Github

  Source code for the RBS calculator.

• Benchling

  Platform for plasmid design, primer design, simple cloning or GoldenGate planning.

• ApE

  A fairly simple but very useful (free) plasmid editor software download.

• Gene Design 3.0

  One-stop shopping for gene construction tools (random sequence generator, reverse translation, etc).

• Optimizer

  Reverse translation with "Guided random" option: outputs an optimized coding sequence that uses all codons in the organism (not just the most common).

• Gene2Oligo

  Very useful when you need to assemble a sequence from individual oligos. (Temporarily Unavailable)

• Random DNA Generator

  Generates a random DNA sequence with defined GC content.

• VectorNTI

  Comprehensive proprietary software for DNA design.

• Geneious

  Proprietary bioinformatics software for DNA design.

• NuPack

  Growing software suite for the analysis and design of RNA secondary structure and other nucleotide sequences.

• SBOL Software Tools

  List of software tools making use of the SBOL data format.

• Cello

  Automatic design for circuits based on input truth-tables.

Nucleotide Sequence Analysis

• Mfold

  RNA and DNA folding algorithms.

• Oligocalc

  RNA and DNA oligo properties.

• ThermoFisher Tm Calculator

  DNA melting temperature calculator for Phusion and others

• ThermoFisher Multiple Primer Analyser

  Calculates Tm, GC content and dimer formation for multiple plasmids.

• NEB Tm Calculator

  DNA melting temperature calculator for Taq, Q5, Phusion and others

• DNA/RNA/Protein Molecular Weight Calculator

  Calculates mass of single- and double-stranded DNA and RNA.

• Graphical Codon Usage Analyser

  Calculates codon usage statistics from a DNA sequence.

• Restriction Mapper

  Finds restriction sites in a DNA sequence.

• Microbes On-line

  Genome analysis tools.

• Online Analysis Tools

  Another portal to good tools.

Protein Sequence Analysis

• Protein Calculator

  Protein Properties.

• SignalP

  Signal peptide cleavage site predictor.

• ProTISA

  Database of confirmed prokaryotic translation initiation sites. (Unavailable)

• ExPASy

  Comprehensive proteomics toolbox.

Alignment Tools

• LALIGN

  Basic sequence alignment tool.

• BLAST: Basic Local Alignment Search Tool

  Protein and nucleotide sequence database alignment tool

• Mobyl@pasteur

  Sequence Alignment and Analysis (ClustalW)

Cytometry Analysis

• FlowJo

  Our preferred proprietary cytometry data analysis tool.

• Cyflogic

  Free cytometry data analysis software.

• FCSExtract Utility

  Converts *.*fcs files to *.*csv files

Information Portals

• CyberCell Database

  Useful data about E.coli K12 MG1655.

• E. coli genotypes in OWW

  Best collection of E. coli genotypes and their meanings.

• BioNumbers

  Database of useful biological numbers.

• Plasmid Databases

  Links to various plasmid sequence resources.

• E.coli Wiki

  Portal for E. coli research.

• Cold Springs Harbor Protocols

  Journal of laboratory protocols.

• Protocols.io

  Open repository for scientific protocols.

• Metafluidics

  Open repository for fluidic systems (liquid handling machines, microfluidic devices and others)

Other Calculators

• BioMath Calculators

  Useful unit conversions.

• Ammonium Sulfate Calculator

  Computes the amount of solid ammonium sulfate required to reach a given percent saturation.

• Centrifugation Rotor Calculator

  Interconverts RPM and RCF for common rotors.

Presentation Tools

• UCSF Chimera Home Page

  Fantastic Molecular imaging tool.

• Instructions for making a movie in Chimera

  Super fast and easy.

• Adobe Illustrator

  Software for easy and high quality figure making.