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GENETIC PARTS

Addgene
Commercial collection of plasmids. Voigt lab parts and plasmids (such as terminators, transcription factors, etc.) are avaailable here.

SynBERC Registry
Public registry of biological parts; mostly for SynBERC members. Voigt lab parts are deposited here.

Registry of Standard Biological Parts
Public registry of standard biological parts; mostly for iGEM

JBEI Registry
Public registry of standard biological parts.

SEQUENCE DESIGN

RBS Library Calculator
Uniform sampling of protein expression for efficient combinatorial optimization. Courtesy of Salis Lab (Penn State).

RBS Generator
Source code for RBS Calculator.

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

GeneDesign 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.

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 nucleic acid systems.

NUCLEOTIDE SEQUENCE ANALYSIS

Mfold
RNA and DNA folding algorithms

Oligocalc
RNA and DNA oligo properties.

Finnzymes Tm Calculator
DNA melting temp calculator for Phusion PCR(nearest-neighbor method)

DNA/RNA/Protein Molecular Weight Calculator
Calculates mass of single- and double-stranded DNA and RNA.

Rare Codon Calculator
Outputs graphical information of the codon usage in your sequence.

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

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

E. coli Statistics
Useful informatin on E. coli

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

EcoliWiki
Portal for E. coli research.

Cold Springs Harbor Protocols
Journal of laboratory protocols

OTHER CALCULATORS

BioMath Calculators
Useful unit converstions

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
Stop using ugly, ad hoc Powerpoint graphics! Make gorgeous vector images in Illustrator instead!

Sythetic Biology Center at MIT MIT Department of Bioengineering MIT
Synthetic Biology Center @ MIT Department of Biological Engineering Massachusetts Institute of Technology