BIT150 – Fall 2008 –
Homework 7 KEY
Due on Thursday November 13th by email to TA: mfaricelli@ucdavis.edu as Hwk7_Lastname
BEFORE the Lab
1. Genetic mapping
Find the subdirectory named ‘Hw7’ in your home directory in plantgenome using PuTTY. This
subdirectory contains a file called ‘rauhall_dat.raw’. Using this data file, create a genetic map with
MapMaker (use the Lab7 guide if needed).
1.1. Start MapMaker and load the data file:
- 5 points What is the size of the scored population?
The size of the scored population is 101 individuals.
- 5 points What is the number of markers used?
The number of markers is 208.
1.2. Using the photo command, save a transcript of your session in a text file.
1.3. Using the sequence command select all the markers (> sequence all), and using the group
command create linkage groups.
- 5 points How many linkage groups are there?
1
There are 5 linkage groups.
- 5 points How many markers are there in linkage group1?
There are 50 markers in linkage group 1.
1.4. Using the sequence command select linkage group 1 markers (> sequence group1) and using
the order command order them:
- 10 points How many and which markers could not be ordered?
Two markers could not be ordered: 9 and 48.
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- 10 points What is the best order without these unordered markers?
3
The best order without these two markers is: 1-2-3-4-5-6-7-8-10-11-12-13-14-15-16-17-1819-20-21-22-23-24-25-26-27-28-29-30-31-32-50-33-34-35-36-37-38-39-40-41-42-43-4445-46-47-49.
1.5. Using the sequence command select order 1 (> sequence order1) and using the map
command map the markers of linkage group 1.
- 10 points Present the map of linkage group1 without the unordered markers. What is the
total map distance for this group?
The total map distance of linkage group 1 without the unordered markers is 129.4 cM.
- 10 points What is the log-likelihood?
The log-likelihood is -406.32.
1.6. Using the try command (> try <marker1> <marker 2> ... <marker n>), try to manually
place the markers that could not be placed in group 1 automatically:
- 20 points What are the most probably locations of these markers?
The most probably locations of markers 9 and 48 are: …8-9-10… and …46-48-47…
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1.7. Using the sequence command, reassign the sequence with the initially unordered markers
placed now in their most likely locations, and using the map command map all the markers for the
new sequence:
- 10 points What is the total map distance now?
The total map distance now is 134.9 cM.
- 10 points What is the log-likelihood now?
The log-likelihood now is -420.87.
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