AVM BIOL368 Week 4: Difference between revisions
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==Purpose== | ==Purpose== | ||
*To continue with our class research and journal projects for the Markham et al. paper | |||
**Continue to learn about sequencing and the similarities and differences | |||
==Methods and Results== | ==Methods and Results== | ||
==Part 1== | |||
*Upload the “visit_1_S1_S9.txt” and “visit_1_S10_S15.txt” files from the [http://openwetware.org/wiki/BIOL368/F16:Week_4 BIOL368/F16 Week 4] page into the Biology Workbench | |||
*Generate a multiple sequence alignment using ClustlW | |||
**Choose 3 clones form 4 different subjects (as shown in table below) | |||
**Photo of tree shown below | |||
**Notice that the clones from each subject group together | |||
**Also note that some of the subjects cluster together (clones from subjects 1 and 2) | |||
***Subject 4 clones may be more related to subjects 1 and 2 | |||
==Part 2== | |||
*Select a sequence form last weeks assignment and align all of the clones | |||
*Calculate S from the alignment | |||
**S is the number of positions where there is at least one nucleotide difference across the clones | |||
*Save the alignment for later use | |||
*Run an analysis for two more subjects | |||
**Table below shows results from these analysis | |||
*Calculate theta for each subject | |||
**(use wolfram alpha for these calculations) | |||
*Within the Clustdist tool generate a distance matrix for one of your alignments | |||
*Choose the highest and lowest pairwise scores and find the % difference | |||
**Repeat this step for each subjec | |||
==Data and Files== | ==Data and Files== | ||
Revision as of 15:29, 20 September 2016
Purpose
- To continue with our class research and journal projects for the Markham et al. paper
- Continue to learn about sequencing and the similarities and differences
Methods and Results
Part 1
- Upload the “visit_1_S1_S9.txt” and “visit_1_S10_S15.txt” files from the BIOL368/F16 Week 4 page into the Biology Workbench
- Generate a multiple sequence alignment using ClustlW
- Choose 3 clones form 4 different subjects (as shown in table below)
- Photo of tree shown below
- Notice that the clones from each subject group together
- Also note that some of the subjects cluster together (clones from subjects 1 and 2)
- Subject 4 clones may be more related to subjects 1 and 2
Part 2
- Select a sequence form last weeks assignment and align all of the clones
- Calculate S from the alignment
- S is the number of positions where there is at least one nucleotide difference across the clones
- Save the alignment for later use
- Run an analysis for two more subjects
- Table below shows results from these analysis
- Calculate theta for each subject
- (use wolfram alpha for these calculations)
- Within the Clustdist tool generate a distance matrix for one of your alignments
- Choose the highest and lowest pairwise scores and find the % difference
- Repeat this step for each subjec
Data and Files
Conclusion
Acknowledgments
References
Weekly Assignments:
Assignment 1 Assignment 2 Assignment 3 Assignment 4 Assignment 5 Assignment 6 Assignment 7 Assignment 8 Assignment 9 Assignment 10 Assignment 11 Assignment 12 Assignment 14 Assignment 15
Individual Journals:
"Week 1: Create Wiki Page" Individual Journal 2 Individual Journal 3 Individual Journal 4 Individual Journal 5 Individual Journal 6 Individual Journal 7 Individual Journal 8 Individual Journal 9 Individual Journal 10 Individual Journal 11 Individual Journal 12 No Week 13 Assignment Individual Journal 14 Individual Journal 15
Class Journal 1 Class Journal 2 Class Journal 3 Class Journal 4 Class Journal 5 Class Journal 6 Class Journal 7 Class Journal 8 Class Journal 9 Class Journal 10 Class Journal 11 Class Journal 12 Class Journal 14 Class Journal 15
