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STRUCTURE-BASED MULTIPLE RNA SEQUENCE ALIGNMENT AND FINDING RNA MOTIFS

Sarver, Michael
http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1151076710

Abstract Details

2006, Doctor of Philosophy (Ph.D.), Bowling Green State University, Mathematics/Probability and Statistics.
With the advent of faster computers and the availability of RNA crystal structures we can now use more information to align homologous RNA sequences. We can take a crystal structure and construct a probabilistic model, based on a SCFG, of an RNA molecule. We construct objects called nodes that modularize the model into small pieces that are more manageable. Using this model we can take sequences that are similar to the sequence in the 3D crystal structure and look for the most probable way that the model could have generated the sequence. Then we can get a detailed description of how each node of the model could have generated the sequence. Using this information we can align sequences. Given a seed alignment we give a procedure to construct a 3D structural alignment quickly. In addition we show how the parameters from the model can be estimated. We also have the ability to do motif swaps using objects called alternative nodes. We have developed an algorithm to quickly search through RNA 3D structures to find motifs. This is accomplished by taking a query motif with m bases and finding the center of the heavy atoms for each base and then rotating it onto candidate motifs that have the same number of bases. Then we measure how good a fit the candidate is to the query by using a discrepancy that we define which involves the distance between bases and their relative orientations. A simple inequality allows us to quickly identify candidates whose discrepancy with the query motif will exceed a cutoff discrepancy. We use this to screen out the vast majority quickly.
Craig Zirbel (Advisor)
Basepair; nodes

Recommended Citations

Citations

  • Sarver, M. (2006). STRUCTURE-BASED MULTIPLE RNA SEQUENCE ALIGNMENT AND FINDING RNA MOTIFS [Doctoral dissertation, Bowling Green State University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1151076710

    APA Style (7th edition)

  • Sarver, Michael. STRUCTURE-BASED MULTIPLE RNA SEQUENCE ALIGNMENT AND FINDING RNA MOTIFS. 2006. Bowling Green State University, Doctoral dissertation. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1151076710.

    MLA Style (8th edition)

  • Sarver, Michael. "STRUCTURE-BASED MULTIPLE RNA SEQUENCE ALIGNMENT AND FINDING RNA MOTIFS." Doctoral dissertation, Bowling Green State University, 2006. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1151076710

    Chicago Manual of Style (17th edition)

bgsu1151076710
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© 2006, all rights reserved.
This open access ETD is published by Bowling Green State University and OhioLINK.