Thursday, 4 August 2011

Interesting articles

This week I've been setting up a new laptop. Shifting from a MacBook back to my beloved Lenovo ThinkPad running Ubuntu. Things have really moved along in the last 4 years (glipper/klipper - how I've missed you!).

Consequently I haven't done anything terribly useful this week other than give a brief talk for the monthly NZ Bioinformatics VC (I don't know what VC stands for yet - must find out). Also, later today I'll give a talk at the BIC Symposium. Fortunately I can reuse one or two slides.

In the absence of anything really useful to say I've spotted a couple of articles this week that have made it to my "I really must read these on the bus to work one day" pile. The first [1] describes some experimental work that shows that Hfq binds to the rho independent terminator of the sRNA SgrS. Since I've recently developed quite an interest in terminators I think I'd better take a look at this result. The second [2] is pulled from Sean Eddy's preprint server. This describes some of his and Diana Kolbe's work on applying HMMER3-like speedups to covariance models. The results appear to be both promising and disappointing. They definitely speed up CMs but to come at a cost to sensitivity, however merging the accelerated CM results with an HMM-filter appears to bring the sensitivity back up to the level of a raw CM, the combined filters appear to be much faster than running a raw CM. So all in all a very promising result. Hopefully this work will be added to the main trunk of Infernal soon.

[1] Otaka H, Ishikawa H, Morita T, Aiba H. (2011) PolyU tail of rho-independent terminator of bacterial small RNAs is essential for Hfq action. Proc Natl Acad Sci U S A.

[2] D. L. Kolbe, S. R. Eddy. (2011) Fast Filtering for RNA Homology Search. In press.

Friday, 22 July 2011

First post

I hope to make this a fairly active blog. Including a weekly roundup of links and articles in the RNA bioinformatics field, an edited diary of my research activities, comments on other research areas, thoughts on bioinformatics and research in New Zealand and anything else roughly professional that seems blog-worthy.