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Scoring RNA Structural Multiple Alignment
Sal LaMarca
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Progress and Future Work
• Progress
– Since I have been busy preparing and studying for final exams this week, I have not
made any progress.
• Future Work
– Next week, I will be attending the IMACS conference at UGA. I will also be presenting
GAMSA (Genetic Algorithm for Multiple Stem Alignment) at the conference.
– Building the RFAM 9.1 in a local copy of mySQL
– Learning more about the RFAM database (which tables and attributes are useful to
query for scoring information)
– RFAM uses Infernal to create covariance models for generating full alignments. I would
like to do more research into this to see how covariance models relates to alignment in
general.
– Implementing a Java program that will start gathering stats (data mining) from a local
copy of RFAM.
– Implementing a Java program that will solve the optimization problem previously
mentioned.
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