Bioinformatics Practice Test 5

1. ______ molecules can simply be identified based on their sequence similarity with already-known sequences.

2. Martinez (1984) made a list of possible double-stranded regions, and these regions were then given weights in proportion to their equilibrium constants, calculated by ______

3. In predicting RNA secondary structure, some simplifying assumptions are usually made, like the _____ structure is similar to the _____

4. The probability model mentioned above was a hybrid combination of HMMs and SCFGs trained on sno RNAs.

5. ______ regions in sequences, such as those in RNA that will form secondary structures, are an example of such context-free sequences.

6. The dynamic programming method produces ____ structure with _____ score.

7. ____ wobble pairs may be produced in these double-stranded regions.

8. These limitations of the Zuker method and other methods have been largely overcome by using an algorithm originally described by Waterman and Byers (1985) for finding sequence alignments within a certain range of the optimal one by modifications of the trace-back procedure used in dynamic programming.

9. Which of the following is incorrect about Phrap?

10. An aspect of the comparative method is to select a __________ structure through consensus drawing.