Chris Rhodes Week 9: Difference between revisions
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*In order to work with the amino acid sequences of the subjects from the Markham paper each subject's [http://bioquest.org/bedrock/problem_spaces/hiv/amino_acid_sequences.php amino acid data] was uploaded onto [http://seqtool.sdsc.edu/CGI/BW.cgi#! Workbench] | *In order to work with the amino acid sequences of the subjects from the Markham paper each subject's [http://bioquest.org/bedrock/problem_spaces/hiv/amino_acid_sequences.php amino acid data] was uploaded onto [http://seqtool.sdsc.edu/CGI/BW.cgi#! 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: [http://www.ncbi.nlm.nih.gov/protein/3319095?report=fasta Kwong], [http://www.ncbi.nlm.nih.gov/protein/6729933?report=fasta Stanfield 1999 Aib], [http://www.ncbi.nlm.nih.gov/protein/6729961?report=fasta Stanfield 1999 His/Ser Loop], [http://www.ncbi.nlm.nih.gov/protein/39654246?report=fasta Stanfield 2003] | *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: [http://www.ncbi.nlm.nih.gov/protein/3319095?report=fasta Kwong], [http://www.ncbi.nlm.nih.gov/protein/6729933?report=fasta Stanfield 1999 Aib], [http://www.ncbi.nlm.nih.gov/protein/6729961?report=fasta Stanfield 1999 His/Ser Loop], [http://www.ncbi.nlm.nih.gov/protein/39654246?report=fasta Stanfield 2003] | ||
*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 these regions for Subject 13 are shown below: | *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. | ||
*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 these regions for Subject 13 are shown inside the green boxes below: | |||
[[Image:CHR_Image1_20111026.jpg]][[Image:CHR_Image2_20111026.jpg]][[Image:CHR_Image3_20111026.jpg]] | [[Image:CHR_Image1_20111026.jpg]][[Image:CHR_Image2_20111026.jpg]][[Image:CHR_Image3_20111026.jpg]] | ||
*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. | |||
Revision as of 14:48, 26 October 2011
Methods
- 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.
- 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 these regions for Subject 13 are shown inside the green boxes below:
- 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.
