-- %TEACHINGWEB%.SwethaAkella - 21 Nov 2011
Homework 7: Information
I worked on this assignment with Daniel Chao.
A high mutual information implies that there is a strong correlation between the identity of the nucleotide at position i and that of the nucleotide at position j. Within the same sequence, the presence of a given nucleotide at position i can predict what nucleotide will occur at position j. The columns with the lowest entropy are most conserved.
The top 20 and top 50 results tell you that the structure of tRNA has high information content, and that the pairs do not have independent mutations. The mutual information values mean that mutation in one base will correlate with mutation in another base in order to preserve the secondary structure of the tRNA, which is vital to ensuring correct codon attachment. The high areas of mutual information are probably encoding regions that base pair to themselves, forming tRNA secondary structures like loops and stems. Therefore the second base must be the complementary base in order to preserve the secondary structure, and must change when the first base changes.
The top 20 probably represents the most vital base pairs to tRNA secondary structure.
A diagram of tRNA secondary structure is given below.
[Bioc 462a Lecture Notes. (n.d.). . Retrieved November 21, 2011, from http://www.biochem.arizona.edu/classes/bioc462/462a/NOTES/Nucleic_Acids/nucacid_structure.html]
In addition, we tried using RNAfold on the first tRNA sequence to see if the base pairing matches up with the highest mutual information pairs. It did not. This could be because the mutual information does not correlate with this, or becaue this software doesnt use the same algorithm to calculate its pairing, or makes other assumptions that throw the base pairing off. We are including the output, with red numbers indicating "spaces" in the alignment.
This figure is a surface plot of the mutual information between the sequences, columns i and j. The peaks correspond to the combinations of i and j with the highest correlation. The peaks probably correspond to a base pairing that is vital to the function of the tRNA.
Copyright © 2008-2013 by the contributing authors. All material on this collaboration platform is the property of the contributing authors.
Ideas, requests, problems regarding TWiki? Send feedback