Salomon Garcia: Week 9: Difference between revisions
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(added max and min for subject 12) |
(added min and max for subject 13) |
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*Once the sequence alignment was done then a ClustalDist Matrix was ran in order to get the max for each of the clones and there particular visits and the matrix for both of the subjects is shown below. | *Once the sequence alignment was done then a ClustalDist Matrix was ran in order to get the max for each of the clones and there particular visits and the matrix for both of the subjects is shown below. | ||
[[Image:distance matrix for subject 12.jpg|thumb|center|450px|Matrix for Subject 12]] | [[Image:distance matrix for subject 12.jpg|thumb|center|450px|Matrix for Subject 12]] | ||
*min difference for subject 12= 1.045 | |||
*max difference for subject 12= 7.03 | |||
[[Image:distance matrix subject 13.jpg|thumb|center|450px|Matrix for Subject 13]] | [[Image:distance matrix subject 13.jpg|thumb|center|450px|Matrix for Subject 13]] | ||
*min difference for subject 13= 1.045 | |||
*max difference for subject 13= 7.03 | |||
*After this matrices were done the next thing that was done was look at each subject and look at two visits at a time for example visits 3 and 4 and then 4 clones were gathered for these visits | *After this matrices were done the next thing that was done was look at each subject and look at two visits at a time for example visits 3 and 4 and then 4 clones were gathered for these visits | ||
*For this portion of the project we sequences and we got a box shaded representation of our clones of Subject 12 and Subject 13 and this is what was seen: | *For this portion of the project we sequences and we got a box shaded representation of our clones of Subject 12 and Subject 13 and this is what was seen: | ||
Revision as of 15:55, 21 March 2010
Formulating our question for the next project and this is what we as a group came up with:
- For this experiment we will be using the Markham et al Paper and we will also be using the Stanfield et al paper. These are the two links for them
- The sequence alignment was done for each of the Subjects in this case it was for subject 12 and subject 13, sequence alignment was done and this is what was shown for both of the subjects. The sequence alignment was done by using Biology WorkBench. These are the images that are seen:
- Once the sequence alignment was done then a ClustalDist Matrix was ran in order to get the max for each of the clones and there particular visits and the matrix for both of the subjects is shown below.
- min difference for subject 12= 1.045
- max difference for subject 12= 7.03
- min difference for subject 13= 1.045
- max difference for subject 13= 7.03
- After this matrices were done the next thing that was done was look at each subject and look at two visits at a time for example visits 3 and 4 and then 4 clones were gathered for these visits
- For this portion of the project we sequences and we got a box shaded representation of our clones of Subject 12 and Subject 13 and this is what was seen:
- Also from the sequence alignment of the 4 clones for each of the visits we get the rooted and unrooted trees and this is what it looks like.
- For this experiment we decided on our article this is a Link to it:http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=78166
- This is a the entire article in pdf file: Article by Lei Chen
