Just had to vent this out. Not really a bad thing, just excited I guess.
SAYANG! I should have gone to Doc Guzman when I had the chance. Malaman ko lang sana agad score ko sa Med I exam yesterday. Haha! GC Mode on.
Prepped really well for that exam, and it's my favorite subject, but it still was tricky pero I'm holding on to the fact that naretain mga inaral/narinig ko during lectures at nagprevail *crossing muh finguhs*.
As medical students, we can't help but wonder why, in every single day, it seems as though the volume of workload keeps increasing exponentially. It is really tiring, and most of us are already beginning to be burnt out. Oh, #MedLife indeed.
But fret not! Because...
Vertigo 2014: Project V
is Coming Soon!
Credits to John Albert Dy
We'll finally have a chance to unleash the party animal inside of us that has been rampaging lately because of all the workload that is burdening us! Hoo boy, I seriously can't wait!
We're not only partying for ourselves, mind you readers. This party is for a cause, and all proceeds will be donated to the Yolanda victims. Remember, we have a duty as Medical Students and future medical professionals to serve our fellowmen!
Last week, I saw this man near Manila City Hall, just right before the underpass under Taft Ave/Lagusnilad. Some people still tried to give him food, water, but he just refused.
I thought of sharing this online, through my social network, just so that this man's pleas may be heard. Apparently, he wants to see his daughters, who are part of the Seventh Day Adventist Church, and to at most likely spend time with them near the end of his life.
Let us do our part in making someone's life and Christmas better.
Let us use the social media to try to help this man.
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.
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.