Lab_3_2010_worksheet

Lab_3_2010_worksheet - Mic 433, Microbial Genomics Lab...

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Mic 433, Microbial Genomics Lab exercise #3 Due February 2 nd or 4 th Name: Mary Ellen Hoinski The goal of this session is to gain some practical experience in assembling and analyzing a consensus sequence, and to solidify your understanding of DNA sequencing chemistry. The contig you build will be assembled from individual sequencing reactions that were performed by a commercial sequencing center. 1. Launch the Sequencher application (found in the applications folder). 2. Choose the Import command from the File menu and choose Sequences . 3. Change the “Files of Type” to All Files , and select the folder of sequences on the computer (the file is on the server and entitled “14 sequences” under MMG433 – Lab 3-). Select all of the sequence files in the folder, and click Open . 4. A project window will appear with the individual sequence icons highlighted. 5. Select the Assembly Parameters button to view the criteria being used to assemble your consensus sequence. Click OK to assemble your sequences using the default Alignment Parameters. Then click on the Assemble Automatically button (make sure that all of you sequence icons are still highlighted). A contig sequence will be generated. Any sequence data that could not be assembled in the contig sequence will still be present as a sequence icon in the project window. 6. Different criteria can be used to assemble your sequences- ranging from liberal (will align more dissimilar sequences) to very conservative (only aligns perfect matches). Try out the various options for aligning your sequences by dissolving your contig by using the Dissolve Contig command from the Contig menu. Then change the Assembly Parameters and click on Assemble Automatically (as in step 6 above) to construct a contig with the new parameters. What does setting the “Minimum Match Percentage” to 100% do when you try to assemble the sequences? Why?
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Lab_3_2010_worksheet - Mic 433, Microbial Genomics Lab...

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