Anthony Poole and I are seeking a talented PhD candidate to explore the evolution and bioinformatics of RNA. Tell your friends!
Closing Date: 30 March 2012
For more, see the information sheet.
For more, see the information sheet.
Showing posts with label bioinformatics. Show all posts
Showing posts with label bioinformatics. Show all posts
Thursday, 8 March 2012
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.
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.
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