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Biologist, M.D.;  Future M.D., FPCP, FPCC, Funny and Awesome guy.

Sunday, December 15, 2013

How to love Genetics and Genomics! Use of CLC Sequencer and BLAST!

One of the tools we are currently using as Medical Students is the CLC Sequencer. It is actually fun to use but it can also be major headache. This post aims to help those using the sequencer and NCBI-BLAST to get what they need.

Things we need:
  1. CLC Sequencer (click here)
  2. A stable internet connection
  3. A sample case (I'm going to use our homework as example)

Now, let us install the CLC Sequencer first, before doing anything. Once everything is in place, we can now begin.

First, open your CLC Sequencer:

The interface is quite simple, anyway, the next thing we need is to load our samples. As seen in my screenshot, I have already saved the samples that I need. To do so, click NEW and then paste your whole sequence into the text box provided:

Name your sequence, then save it (click the save button at the menu). When you are done, your sequence would then appear  on your screen. 

 Next, click the following on your CLC Sequencer:

Find the longest Open Reading Frame (ORF) by following these steps:

Choose these options (unless you have instructions otherwise), then Click Next

 Confirm, and click FINISH

This table would appear and show you which possible ORFs there are available so you can choose. Remember, the longest ORF is what we need (as highlighted above). 

Using the table as a guide, look for the sequence number (in my case it is 1010 to 1831). Remember, each line consists of 60 nucleotides with 10 in each column. The one I highlighted above is shown to be from 1010 to 1831, which CLC said was my longest possible ORF.

Next, copy and paste that particular sequence and create a new sequence in the CLC.

Your next step now is to translate it to protein by clicking the menus posted above.

Tada. Now you have your protein sequence. Its now time to fire up your web browser and point it to NCBI-BLAST (blast.ncbi.nlm.nih.gov)

Click on PROTEIN BLAST and paste your protein sequence in the text box seen below:

You will find the following results. What you need is the result with the highest (99-100%) Query Value, and it will usually be the first one. 

Click the Accession Value link, and you will be linked to this page:

Look for the title of the study where your protein sequence is related to. You can now infer the case that was given to you. In my case, it is Phenylketonuria.

It's fun to use this CLC viewer, albeit the hardships you gotta go through just to understand and be able to use this tool properly. Once you get the hang of it, however, it'll be smooth sailing from here on out.

Hope this helps!

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