Chris Rhodes Week 9: Difference between revisions

Revision as of 15:23, 26 October 2011

In order to work with the amino acid sequences of the subjects from the Markham paper each subject's amino acid data was uploaded onto Workbench
Individual ClustalW alignments were performed between all the amino acid sequences of a particular subject and the amino acid sequences of the proteins used in the Kwong and Stanfield papers in order to identify regions of possible functional significance in the amino acid sequences of the subjects. The Kwong and Stanfield sequences can be found here: Kwong, Stanfield 1999 Aib, Stanfield 1999 His/Ser Loop, Stanfield 2003
Since our primary understanding of the functional significance of the gp120 amino acid residues is based on the Kwong and Stanfield papers our results can only be interpreted if they coincide with the data we've gathered from these papers. Therefore using the protein data of the sequences from the Kwong and Stanfield papers we will find the regions within the Markham amino acid sequences whose results can be related back to the data of the Kwong and Stanfield papers. This experiment will only look at amino acid changes that occur within these regions
Regions of functional significance were determined as highly conserved consecutive sequence areas in the alignments between the subject and the Kwong and Stanfield sequences. Examples of the determination of these regions for Subject 13 are shown below where the regions of functional significance are found within the green boxes.

For Subject 13 the regions of possible functional significance were found to be residues 1-23, 37-51, and 61-95 of Subject 13's amino sequences. Any significant changes in the residues of the Subject 13 amino acid sequences that occur within these region will be considered to be of functional significance.
For each subject, both the amount of changes that occur and the exact amino acid substitution that occurs for each change within the regions of functional significance will be recorded. Based on the type of amino acid change that occurs for each residue the change will be hypothesized to be either functionally significant or non-functionally significant.
Phylogenetic trees of the amino acid sequences, generated through ClustalW alignments, will also be used to aid in determining which amino acid sequences to use when comparing for functional differences.

Subject 13

Rooted Tree

ClustalW alignment of visit 4 and 5 sequences with region of functional significance shown in red.

@@ Line 10: / Line 10: @@
 ==Results==
 '''Subject 13'''
 Rooted Tree
 [[Image:CHR_Image5_20111026.gif]]
 ClustalW alignment of visit 4 and 5 sequences with region of functional significance shown in red.
 [[Image:CHR_Image4_20111026.jpg]]
 ==Links==
 {{Chris H. Rhodes}}