Finding Post-translational Modifications:

PhosphoSitePlus is very comprehensive and has a good search function to allow you to find sites of phosphorylation, ubiquitination, acetylation, and other modifications in proteins of interest.  It seems to be very comprehensive.

Phosidia seem redundant with PhosphositePlus, and only tabulates phosphorylation, ubiquitination, and glycosylation, but it is worth looking at just in case.

DNA cloning and plasmid organization software

We use the following packages (Mac and PC versions are available):

ApE (A plasmid Editor), which can be dowloaded here.  


SnapGene, which can be downloaded here.  Check with Rita for a registration code.

RNA structure:

NUPACK can be downloaded here.

mFOLD can be accessed here.


KineFold (for animating RNA folding) can be accessed here.


Protein-protein interactions:

BioGRID: an online interaction repository.

Molecular INTeraction Database (MINT): Website has an interactive viewer for visualizing interaction networks.

Database of Interacting Proteins (DIP)

Biomolecular Interaction Network Database (BIND): Database of molecular interactions, complexes, and pathways from data submissions and scientific literature.

Agile Protein Interaction DataAnalyzer (APID):  Integrated platform for exploring PPIs from experimentally validated data.  Incorporates data from BIND, BioGRID, DIP, HPRD, IntAct, and MINT. 

Useful numbers for biologistshere

Online protocols: has a lot of useful protocols and techniques.  Many movies are shown to demonstrate procedures.

The Journal of Visualized Experiments (JOVE) has movies for many detailed protocols for advanced techniques, including several useful culturing protocols.  It is worth searching their movie library to see how they recommend performing various protocols.

Repositories of embryo/animal-wide gene expression patterns:


The Gene expression database from Jackson Labs allows you to search for gene expression by gene, tissue, Affymetrix gene identifier, and several other parameters.  Click "Expression" from this page.

Mouse atlas of gene expression

eMap Edinburgh mouse atlas

Guidelines for performing specific techniques

For qRT-PCR experiments, we follow the MIQE (Minimum Information for Publication of Quantitative Real-Time PCR Experiments) guidelines.  These guidelines affect how to peform qRT-PCR, and how to describe them in the Methods sections of papers. 

Antibody companies with "small size" aliquots:

Ordering Posters:  Should be ordered 4 days in advance.