Every Thursday evening, the homepage at Nature Protocols gets updated. We highlight a new protocol, add a new image in the “upload your own image” slot, and add a few more protocols to the list of Network Protocols in the “Read Highlights from the Network” sidebar. At the same time, new protocols (usually about 8) are added to the current issue.

Inevitably mistakes creep into this process, can you spot the mistake on the current homepage?

The new featured protocol

The latest featured article, which means that it is freely available, is for a fast walking method for single-tube transposon mapping. This is a method of flanking sequence retrieval that has been applied to map the insertion of transposons. It is based on the original Universal Fast Walking (UFW) method that was published by the authors in their 2002 ‘Gene’ paper

However, in this protocol, the original method can also be enhanced by the use of agarase, to allow composite nucleotide sequences to be unscrambled. This protocol would also be applicable to general genome walking and cDNA walking, as well as viral and other insertional element mapping.

Finally, on an entirely unrelated and unscientific note, I think that a UFW protocol is very timely, as I seem to have found myself Universally Fast Walking home from the station every day this week in order to combat the effects of the drop in temperature we have suffered! On the upside, the weather has provided some beautiful sunsets here at work…

[Thank you to Hannah, our resident expert, for supplying the text for this section.]

The new image

This was supplied by L. A. Donaldson, L. Grace, and L. Holland.

Can you guess what it is?

The new Network Protocols

This week, I would like to highlight a series of Network Protocols uploaded by the Raghava group. These are bioinformatics methods for predicting whether or not a peptide is antibacterial,
a protein is mitochondrial,
a protein is likely to be allergenic,
and a protein is likely to bind to MHC class II molecules.

Ask Aunty Bron

What is the difference between Nature Methods and Nature Protocols?

This is a really good question! There are two important differences:
(1) Nature Methods publishes primary research, that is, methods that are new and have not been published before, while Nature Protocols publishes (hopefully) reliable methods that have already been used to generate results in primary research papers. Most of Nature Protocols’ content is commissioned.
(2) Nature Methods are formatted as a normal article, while in Nature Protocols, the procedure is written as a series of number steps in the active tense.

Protocol manuscripts are also structured slightly differently: The headings are Abstract, Introduction, Materials (Reagents, Equipment, Reagent Setup and Equipment Setup), Procedure, Timing, Troubleshooting, and Anticipated Results.

There are also cute little callouts.

Editorial Blooper

The invitation for the currently featured protocol, written by Professor William M. Gelbart from the Department of Molecular and Cellular Biology, Harvard University, was originally sent to William M. Gelbart, Professor of Chemistry at UCLA… who gracefully declined.