16S rRNA Gene Sequence Aligner (Online)

Here's an online sequence aligner for 16S rRNA gene sequences that I heard about from Ruth Ley at the MBL workshop. It solves one of the problems with the ARB aligner - namely that the ends of the sequences are scattered all over the place and you have to manually adjust them.
The only downside is that this aligner aligns the sequences to other databases such as Phil Hugenholz's. Still, nice to avoid the problem with the ends.


http://greengenes2.lbl.gov/cgi-bin/nph-NAST_align.cgi

Website for SuPER PCR

I had an idea to create a website specifically for SuPER PCR users. So, I just appended another blog page to mine and it will hopefully serve as a node for people interested in the method and looking for advice and any updates. It can be found here: http://www.superpcr.blogspot.com.

Other than that, I am busy running phylogenetic analyses on some sequence data . I am trying out a new (well , for me) phylogenetic package call Mr. Bayes. We'll see how it goes - it is going to be running for a few days here!

SuPER PCR and Streptomyces Paper

Well, sorry I haven't updated the site in a while. I've been at a Molecular Evolution class in Woods Hole, MA. The main coursework of the class has just finished, and now I'm here for one more week to analyze some of my data from my Ph.D. work. Unfortunately, I'm a bit sick and have been so for a few days. Hopefully a good nights' sleep will take care of it.

Anyway, I'm very excited. My methodology paper with Dror was just published in the journal of Applied and Environmental Microbiology. It's a nice little technique that we developed a while ago and have been trying to get the word out. The method is called Suicide Polymerase Endonuclease Restriction (SuPER) and is meant to operate as a prior step to PCR and other molecular analyses. The method helps deal with a problem frequently found in environmental studies - the predominance of a single type of DNA that overwhelms the detection of other types of DNA.

Also, my paper with Ehud (now a Ph.D. student at the Technion in Haifa) was just published online in the journal Microbial Ecology. So, overall, a good publication week! This article is about the effects of compost amendment to soil on bacteria from the genus Streptomyces developing on plant roots of plants grown in such soils.