GENETIC PARTS
BioPartsDB
BioParts Database (for biocircuit design)
Registry of Standard Biological Parts
Public registry of standard biological parts; mostly for iGEM
Addgene
Nonprofit plasmid repository for public sharing
Addgene - Wang Lab plasmids
Addgene collection of plasmids deposited by the Wang Lab
SEVA
Standard Europen Vector Architecture
SynBERC Registry
Public registry of biological parts; mostly for SynBERC members
JBEI Registry
Public registry of standard biological parts
RDBSB
Registry and database of bioparts for synthetic biology
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
Reverse Complement
Converts a DNA sequence into its reverse, complement, or reverse-complement counterpart
Integrated Microbial Genomes
Comparatively analyze genome data by gene, genome and function
NUCLEOTIDE SEQUENCE ANALYSIS
Mfold
RNA and DNA folding algorithms
UNAfold
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
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
E. coli Statistics
Useful informatin on E. coli
E. coli genotypes in OWW
Best collection of E. coli genotypes and their meanings
EcoCyc E. coli Database
Encyclopedia of E. coli Genes and Metabolism
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
Gibson Calculator
Primer design for Gibson ligations (KT)
Hill Coefficient Calculator
Calculates Hill coefficient from tab-delineated data
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!
BoxPlotR
A web-tool for generation of box plots
Jalview
One of the most widely used applications for visualising and analysing DNA, RNA and protein multiple sequence alignments. It is designed to enable anyone working with protein, RNA and DNA sequences to investigate their structure, function and evolution, and create high-quality figures for publication. Open source, developed by Dundee Univ
Other Useful Resources
Journal Sites
Nature Nature Biotechnology Nature Chemistry Nature Chemical Biology Nature Methods Nature Microbiology Nature Communications Nature Biomedical Engineering
Science Science Translational Medicine Science Advances Cell Cell Host & Microbe Molecular Cell Cell Systems Cell Reports Molecular Systems Biology PLOS Biology
PNAS Nucleic Acids Research ACS Synthetic Biology Analytical Chemistry Biosensors & Bioelectronics ACS Sensors JACS Angewandte Chemie Advanced Materials AFM