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1) to determine what kinds
of mutations occur in a gene and two adjacent spacers
1) to determine what kinds
of mutations occur in a gene and two adjacent spacers, 2) to
compare mutation rates of the gene and spacers to see if they
differ and if they conform to expectations, and 2) determine
relationships among a small group of three species using their
DNA sequences
the links for the DNA sequences:https://www.ncbi.nlm.nih.gov/nuccore/MZ061862.1?re…,
https://www.ncbi.nlm.nih.gov/nuccore/MZ061863.1?report=fasta,
https://www.ncbi.nlm.nih.gov/nuccore/MZ788653.1?report=fasta.
Highlight all three of the sequences in the text file andcopy them; make sure that you do not copy any blank lines orspaces before or after them.B. Go to www.ebi.ac.uk/C. The name of the alignment program you will use is “Muscle.”Click on “Services” at the top of the EMBL-EBI page, enter theprogram’s name into the search field, click on the Search button,and click on the program’s name in the one result you should get.D. On the Muscle page, paste your copied sequences into thespace provided at “Input sequence”. Then scroll to the bottom andclick on the “Submit” button (you do not need to change anythingin “Parameters”).E. After a few minutes (or less) the alignment tool will finishand you will see your aligned sequences in a fancy color-codedformat. Click on “Tool Output” to see the sequences in adownloadable form and click on “Download”. You will get a textfile of the aligned sequences; this is the document that willbecome your Figure 1.F. Determine which species corresponds to each of the threesequences in the aligned text file by comparing the Genbankaccession numbers in the two text files
Add up the total number of mutations (point mutations andindels) in the first spacer. Then do the same for the 5.8S gene,and then for the second spacer
Calculate the mutation rate (average number of mutations pernucleotide position) for each of the three regions. To get themutation rate, divide the total number of mutations in the regionby the length of the region.F. Based on differences among the sequences, determine howclosely related the three species are to each other. This is doneby making three pairwise comparisons among the sequences (firstand second, first and third, second and third). In each pairwisecomparison, determine how similar the two sequences are bycounting how many DNA sequence differences there are between them(include both point mutations and indels)
Introduction. Should include some basic backgroundinformation on DNA and mutations and a statement of the objectives of the assignment . Methods and Materials. Describe what you did. You need toinclude enough detail that someone else should be able to do theexperiment the same way you did.D. A combined Results and Discussion section. This sectionshould describe all your results and conclusions. It shouldcontain the following things:1. The aligned length of each spacer and of the 5.8S gene.2. The total number of mutations in each of the threeregions.3. a) How many mutations in each region are transitions,transversions, and indels, and b) based on what you have learnedabout molecular evolution, whether the relative numbers oftransitions and transversions conform to expectations.4. a) The mutation rate for each region, b) a comparison ofmutation rates of the gene and the spacers, and c) based on whatyou have learned about molecular evolution, whether the relativegene and spacer mutation rates conform to expectations.5. The results of the three pairwise comparisons, and therelationships among the three species suggested by the pairwisecomparisons (how closely and how distantly they are related toone another).E. One figure. It should contain a printout of the threealigned sequences with the boundaries of the two spacers and the5.8S gene marked. It should also have a caption describing whatit contains and identifying which species each sequencecorresponds to
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