Genetic Mapping Homework for BIT150, Fall 2008, Assignments of Bioinformatics

Download Genetic Mapping Homework for BIT150, Fall 2008 and more Assignments Bioinformatics in PDF only on Docsity! BIT150 – Fall 2008 – Homework 7 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? - 5 points What is the number of markers used? 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? - 5 points How many markers are there in linkage group1? 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? - 10 points What is the best order without these unordered markers? 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? - 10 points What is the log-likelihood? 1.6. Using the try command (> try <marker1> <marker 2> ... <marker n>), try to manually place the markers that could not be initially placed in group 1 automatically: - 20 points What are the most probably locations of these markers? 1