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Tools for research

Entrez Gateway is the parent thread for PubMed and BLAST. Start here!

Primer design: Use Primer3 to design your own or download pre-designed sequences for real time RT PCR for human and mouse transcripts from Primer Bank. For validating Affymetrix data using real time RT PCR, one option is to design primers against the transcript target region, obtained from NetAffx. You can predict product sizes based only on primer sequence information using this.

Sequence manipulation: To align two sequences, I use this. To convert nucleotide sequences into reverse, complement or reverse complement, check this out. You need to delete all the text in the box, even the hidden stuff! To figure out how many exons a gene might have, check out Evidence Viewer. To reduce something to ACTGs, this filter is useful.

Microarray analysis: I use dChip and Onto Tools, and NetAffx.

Viral vectors: Mike McManus’ website is good on lentivirus construction. And loads of other things including RNA interference. The Tronolab website is good, too. You can buy plasmids for lentiviral vectors from Addgene.

RNA interference: Need to design siRNAs or shRNAs? Mike McManus’ website is good again.

Cloning: Here’s one website. Here’s another. And another. More websites than you can shake a stick at. Promega have some good freebie handouts too. If you need to find restriction sites, check this out. If you want to know what size products to expect after restriction digestion, voila. If you need to find common primer annealing sites for sequencing, click here.

Full length cDNAs in a plasmid: (e.g. for electroporation or to make a viral vector to overexpress a gene of interest)? Clonehunter is here. Also check out NIH. The Mammalian Gene Collection sell cheaply via ATCC.

Microscopy: Fluorescence Spectra Viewer—useful for figuring out what fluorophores will work with a given microscopy filter set. NIH Image is a good image processing tool.

File transfer:  Need to send a file that’s too big for email?  Use this website.

Career information: nextwave.


For conversion of RPM to RCF (g) or vice versa, check this.

There are various atlases of gene expression of the nervous system available, including GENSAT

Animal behavioural assessment: Videos of behavioural testing in various animal models of injury (Schallert lab). Also ask me to borrow Ian Whishaw's excellent DVD.


Quick Links

Nature Protocols manuscript and links

Publications as PDFs

Media coverage as PDFs