-- %TEACHINGWEB%.KamranAli - 24 Oct 2009
Homework 5
Part 1: Written Part
- If you align a sequence with unknown structure and sequence with known structure and find that the sequences are homologous. This information can inform your prediction of the structure of your sequence as the structures are likely also homologous. In fact large sets of structural alignments are often used to test the effectiveness of a sequence alignment method.
- Directed Evolution randomly mutates a sequence and hopefully some of your mutants will have some altered or novel function. An alignment of these mutants with the original gene can reveal highly conserved regions necessary for function, less conserved regions, and potential sites for mutagenesis that may lead to interesting changes in protein function.
- Constructing a local alignment of the gene and the host genome will help you determine if there was gene transfer. If there was no gene transfer the alignment at the gene will likely be very gappy.
- Areas in the genomic sequence where the regulatory element sequence aligns are the most likely sites for regulatory elements.
Part 2: Nussinov
- Perl code is on bspace.
- Analysis:
| Sequence Length (nucleotides) |
Runtime (s) |
| 8 |
0.029 |
| 16 |
0.031 |
| 32 |
0.047 |
| 64 |
0.143 |
| 128 |
0.46 |
| 256 |
3.052 |
| 512 |
23.913 |
| 1024 |
194.835 |
The black line on the graph is a cubic polynomial and roughly approximates the observed runtimes. This demonstrates that runtime grows at a cubic rate with respect to sequence length which confirms our theoretical predictions for the runtime of the Nussinov algorithm.
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