Using the command line to analyze DNA sequences and detect chimeras was an interesting experience. I learned a major error in how PCR works (i.e. it creates chimeras), but also how to fix it, in reference to measuring richness, using the command line. I think the most important thing I learned was only said in passing by Dr. Mueller. He said that using bioinformatics, one can do a couple of weeks’ or month’s worth of lab work in an afternoon. Time is the limiting resource in most of the laboratory work I have done and the idea of being able to save that much time through the application of bioinformatics seems enticing. I will be continuing to learn bioinformatics in the future and have looked at a master’s program OHSU offers it.
Here is a link to it – https://www.ohsu.edu/school-of-medicine/medical-informatics-and-clinical-epidemiology/bioinformatics-and-computational-0
As far as helping other students goes, I think the most helpful thing I learned was how to do basic command-line skills like how to copy-paste with a PC and how to bring up your previous command with the up arrow. These seemed to save a lot of time and made it easier to go back and find syntax and/or spelling errors. This was my first time working with bioinformatics but determining where the chimera’s parent changed made a lot of sense simply because there should be all of one parent’s alignments on one side, and all of the other parents on the other side of it. It was somewhat difficult for me to understand how the USEARCH function would tell the difference between an unsequenced relative to a parent versus a true chimera but Dr. Mueller helped me with this. The distribution of the alignments (all A’s on one portion and all B’s on another) is a major way USEARCH is able tell this. If they are interspersed throughout the sequence then the “parent” sequences may just be relatives and the query an unsequenced relative rather than a true chimera. My eureka moment was when I got a 127 error during the chimera detection project and I just closed PuTTY, opened it back up, ran the script again, and got a 0 output! I have no idea why that worked but I will be using that in the future!
All in all, bioinformatics is cool, and being able to eliminate a lot of the artificial richness that chimeras bring along with them was useful. I feel like the bioinformatics stuff we have done in class thus far compliments field/lab work but I would like to do more in the future that is able to eliminate some of it, as Dr. Mueller talked about in the first bioinformatics class.
