CPGR Workshop â Tutorials Tutorial 1 â Evaluating loci to be ...

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14. Click the large ‘BLAST’ button to start the search. In a minute or so you

should get a BLAST results report loaded into the browser. A portion of which is

shown below. You can also copy and paste the BLAST report into notepad and

save it. You may want to refer to the BLAST report during the lecture tomorrow.

15. Although we will cover the blast report in detail tomorrow, you should be able

to determine if the locus is unique to the Xanthomonas pathovar? Is the locus a

good candidate for marker development. Why or why not?

16. Now, press the back button on the browser to go back to the BLAST input

page. Change the expect threshold to 10 and run the search again. Does the

BLAST report change? Record your observations for discussion tomorrow.

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12. Now we have to choose the correct BLAST program. We will discuss this in more detail tomorrow. For now choose blastn, which searches a nucleotide sequence against a nucleotide database of sequences. 13. Set the expect threshold to 1e-5. In this case, I also set the max target sequences to display at 10 to prevent a large amount of data coming back from the BLAST server.

14. Click the large ‘BLAST’ button to start the search. In a minute or so you should get a BLAST results report loaded into the browser. A portion of which is shown below. You can also copy and paste the BLAST report into notepad and save it. You may want to refer to the BLAST report during the lecture tomorrow. 15. Although we will cover the blast report in detail tomorrow, you should be able to determine if the locus is unique to the Xanthomonas pathovar? Is the locus a good candidate for marker development. Why or why not? 16. Now, press the back button on the browser to go back to the BLAST input page. Change the expect threshold to 10 and run the search again. Does the BLAST report change? Record your observations for discussion tomorrow.

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Page 3 and 4: 6. Now you have a GenBank record fo
Page 5: 10. Now that we have the sequence o

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