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.


  1. No need to move for glipper:

  2. I knew someone would find something like that. ;-)

  3. Further support for reference [1]:
    Evelyn Sauer and Oliver Weichenrieder (2011)
    Structural basis for RNA 3′-end recognition by Hfq.