Online Resources

Databases

EcoCyc
All you need to know about genes and proteins in E. coli

Saccharomyces Genome Database
As above, but for yeast

The Promoter Database of Saccharomyces cerevisiae
List and sequence of some commonly used yeast promoters

Addgene
Database of plasmids available for sharing

KEGG (Kyoto Encyclopedia of Genes and Genomes)
Metabolome database

BRENDA
Information on characterized enzymes

Quartzy
Online database for lab strains, plasmids, and protocols

PDB: Protein Data Bank
Repository of protein crystal structures

NCBI/PubMed
NIH’s repository of all information about biological system

Software & Analysis Tools

SnapGene
Freeware vector map annotation tool/database

PlasMapper
Identify common features in a plasmid sequence

OligoCalc
Helps determine properties of an oligonucleotide sequence

mFold
RNA secondary structure prediction tool

Berkeley Drosophila Genome Project
Tool to identify eukaryotic or prokaryotic promoters in a DNA sequence

Biomass Feedstock Composition and Property Database

Igor Kurnikov’s list of Molecular Modeling Software
List of molecular modeling software

Mendeley
Best way to organize, and store all you research literature. With the helper note-taking-enabled iOS app, it really saves on printing.

Serial Cloner
Tool for modifying genes and performing in silico reactions to evaluate DNA manipulations

NEB Interactive Tools
A variety of tools useful for molecular cloning, including: Tm calculator, NEBiocalculator (ligation calculator, DNA/RNA unit conversions, etc.), double digest finder, restriction enzyme finder, etc.

Leave a Reply