Roadblocks and Rollercoasters

By Laura Hinsch

As the annotation of Phatniss came to a close and our own personal projects came to fruition, I hit the ground running. SirSheldon was a lucky little phage. He didn’t finish first at the phage Olympics, but when he shot for the moon, he landed amongst the stars and was sequenced anyway. As you might recall, SirSheldon had respectable statistics last semester. His DNA was strong and quite evidently present. Over break, he left the lab to be sequenced, his genome was sequenced using Illumina sequencing, a type that dispenses a high number of reads. When SirSheldon’s sequence returned it arrived as a large compilation of base pairs and read information. For me, this was very different and more complex than the arrival of Phatniss. Unlike Phatniss, SirSheldon’s genome had not been assembled. The responsibility of assembling his genome fell on my shoulders. An arduous task at hand, I learned how to compile a file with a smaller number of reads and assemble the genome using the Gene DeNovo assembler. When my 25k, 50k, 100k and 150k assemblies were finished, I discovered an uncanny trend in my assemblies. I would always have a primary contig with a generous number of base pairs, approximately 80k. However, I would also have several other contigs ranging from 2,000 base pairs to 100. This was unfortunately troubling and I was advised to BLAST the extra contigs. To my great distress, the results came up with a direct hit to Phatniss. I felt like a father who had raised his child for ten years, just to discover that the child was not his. Defeated, I began to pick up the pieces of my shattered project. The first step on the road to recovery was to run a PCR and discover where the Phatniss genome contamination occurred.

Today was my first day back in the lab since last semester and even though my project is still fragmented and broken, there is something truly comforting about having that micropipette in hand as you do nine-fold dilutions. I look forward to hopefully completing the assembly and annotation of SirSheldon, and I know that even with my setbacks, it’s worth it because I will have a phage to call my own.

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About lhinsch1

Hi! I'm just a poor college student trying to navigate the world of culinary experience with poise and an economical outlook.
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