Recently, as part of my work characterizing plant cell walls, I needed to express a few proteins that would serve as molecular probes. I read a couple of papers and the boss man gave me the green light. The first step is to find the protein sequence and have the gene synthesized so that we can transform it into some E. coli and start expression tests. So to order the synthesized gene I went to the paper that described the protein, scoured the methods, and found that–as expected–they didn’t give the sequence, they simply referred to a previous paper, which referred to a previous paper, and after going down the rabbit hole I finally found the original reference.
1 Introduction 1.1 Essential Tools and Basic Knowledge 1.1.1 Fasta Format 1.1.2 Notepad++ 1.1.3 BioEdit 1.1.4 Unix Terminal 1.1.5 R 1.2 Getting Data 1.2.1 Keyword Search 1.2.2 BLAST 1.3 Cleaning Data 1.3.1 Concatenate Sequences 1.3.2 Remove Duplicate Sequences 1.3.3 Remove False Hits 1.3.4 Trim Extra Domains 1.3.5 Clean up Names 1.4 Conclusions Disclamer: I’m a trained microbiologist/biochemist, which means most of my bioinformatics knowledge was self-taught.
Disclamer: I’m a trained microbiologist/biochemist, which means most of my bioinformatics knowledge was self-taught. What you’re about to see may not be pretty; the code might be janky or the workflow inefficient. But I have gone through countless hours of googleing, reading, and trial/error to learn this, and it works pretty well for me, so it might for you too. Let me know if you spot errors or have suggestions for improvement!
Well, as promised to follow up my Friday Fails post, here’s a Saturday Success. I had a few science successes this week, like collecting some decent AFM images, learning purrr, or posting on this blog and tweeting (two of my outreach-related goals). But what I’m most proud of, is my recent decision to try reducing my plastic use and the waste I generate.
It gives me so much anxiety and makes me feel very helpless and sad to think about the future of our planet.
Welcome to a new series: Friday Fails. I’m aiming for weekly consistency with this one, but some may weeks I may just Tweet my fails (and inevitably miss some posts, look out for an upcoming Friday Fail on not posting the previous week!). The reason for this series is not to denigrate myself, it’s in the interest of honesty. The point is to showcase the real me, or at least a less shiny version… shiny as in that girl in your lab who has an NSF grant, 3 papers, and manages to show up every day looking 💯; or that professor who got tenure while raising 2 kids and publishing her ass off.
Hi, I’m Will, welcome to my blog! If you’re reading this, it’s probably because you should be writing 😜. But go ahead and congratulate yourself, because you’ve chosen an excellent way to procrastinate. In fact, I should be writing right now too (well actually I am writing right now, but not the right writing… ya’know?), so let’s procrastinate together! I think that’ll be my motto, Let’s procrastinate together!, because (A) everything is better with friends 😄, and (B) it’s a scientific fact that 95% of my blog posts will be written when I should be working on something else.