Joint Loop End Modeling Improves Covariance Model Based Non-coding RNA Gene Search

author: Jennifer A. Smith, College of Engineering, Boise State University
published: Oct. 14, 2010,   recorded: September 2010,   views: 2357


Related Open Educational Resources

Related content

Report a problem or upload files

If you have found a problem with this lecture or would like to send us extra material, articles, exercises, etc., please use our ticket system to describe your request and upload the data.
Enter your e-mail into the 'Cc' field, and we will keep you updated with your request's status.
Lecture popularity: You need to login to cast your vote.


The effect of more detailed modeling of the interface between stem and loop in non-coding RNA hairpin structures on efficacy of covariance-model-based non-coding RNA gene search is examined. Currently, the prior probabilities of the two stem nucleotides and two loop-end nucleotides at the interface are treated the same as any other stem and loop nucleotides respectively. Laboratory thermodynamic studies show that hairpin stability is dependent on the identities of these four nucleotides, but this is not taken into account in current covariance models. It is shown that separate estimation of emission priors for these nucleotides and joint treatment of substitution probabilities for the two loop-end nucleotides leads to improved non-coding RNA gene search.

See Also:

Download slides icon Download slides: prib2010_smith_jlmi_01.pdf (726.4┬áKB)

Help icon Streaming Video Help

Link this page

Would you like to put a link to this lecture on your homepage?
Go ahead! Copy the HTML snippet !

Write your own review or comment:

make sure you have javascript enabled or clear this field: