How to BLAST in CLC:

• Toolbox → BLAST search → NCBI BLAST⇒⇒⇒⇒


• Choose raw data to us (already saved on CLC).


• The first thing you'll see on BLAST will be a page of green lines with strings of number beside them. ⇓

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• Look to the bottom left of the page, under the strings of numbers for this button (show BLAST table):




• Click on it, and you can now see a page of hits from BLAST. It will show you the top hits from the BLAST search. Double click any of the hits to bring up what appears to be a consensus sequence of your raw data and the double clicked hit. ⇓
  

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To Create an Alignment:

• Toolbox → Alignments and Trees → Create Alignment⇒⇒


• Choose two or more sequences to create an alignment from.


• The alignment will look like a very colorful string of letters, shown in rows. ⇓
  

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To Create a Tree:

• Toolbox → Alignments and Trees → Create Tree⇒⇒


• Choose an alignment to create the tree from.


• The tree may have more or fewer branches than this one, depending on how many sequences are in the alignment you use to create it. ⇓
  

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Tips for using CLC:

• When learning how to use CLC, use all default settings unless otherwise noted in my instructions.


• At any time, you can press this buttonto make comments on what you are doing. This is a good way to keep track of what you are doing.




• When creating an alignment, clicking this button will show the alignment without all of the bright colors. Every match is shown in white and every non match in pink. This will help in fixing errors.






CLC Procedures is the last step of the Thermus process!




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