From Bio Lab to Computer Lab

Phage Hunters is back and has been working on annotating Manatee’s genome for three weeks now. It used to take 3 hours to annotate three possible genes, but now we are all pros. We can get 10 genes annotated in 30 minutes (give or take). So far we have annotated 55 out of 92 possible genes!
This week something new crossed our computer screens: reverse genes. Every genome is made up of genes, but those genes can be read in two different directions – forwards or reverse. Up to gene 37 or so all of Manatee’s genes had been forward, but now we have reached the part of the genome where the genes are in reverse. Luckily, this change in direction does not change much of our analysis. We still look at the length, Shine Dalgarno score, coding potential, Blast hits, and HHpred, but this change in direction does affect the start and stop codons and the gaps between genes. With forward genes the start codon is downstream of the stop codon, however with reverse genes the start codon in upstream of the stop codon – the gene will be read in the opposite direction. We have to be extra vigilant to where we believe a gene starts and stops. When calculating gaps or overlaps between genes, we used to look at the gap between the stop of the gene before and the start of the next gene (i.e. stop of gene product 3 – start of gene product 4 will give us the gap or overlap between gene 3 and gene 4 of a forward gene). With reverse genes we have to look at the start of the gene before and the stop of the gene after (i.e. the stop of gene product 6 – the start of gene product 5 for a reverse gene).
When we were annotating Manatee’s forward genes, we would notice that there was a spike in coding potential running in the opposite direction. While this is interesting to note, it is highly unlikely that a reverse gene would suddenly pop up among forward genes. This is because to suddenly stop translating a forward gene, translate a reverse gene, and then go back to translating forward genes is not very efficient for a phage (or any organism) – and every phage wants to be as efficient as possible. So if we see some forward coding potential as we annotate the reverse genes, we will have to deeply consider whether or not we think there could be a forward gene there.
It has been quite a change to move from the lab to working on computers. Every time we do group annotations and the lights go down, I look around the room and see faces illuminated by glowing computer screens. Also not being in the lab has allowed for snack time, which everyone always loves. My favorite part though is the group atmosphere. Last semester in the lab, I hardly ever saw or interacted with people on the other side of the lab. My focus and my project were at my lab bench and on my phages. The only group meetings were every couple of weeks so we could do a group check in and talk about what we were each doing. Now every time I walk into Macaulay 101, I see all my fellow Phage Hunters. Each class period we work together to annotate Manatee’s genome and it is all together that we will come up with a final annotation.

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