Thank you for your question! Clustal Omega is a software that aligns and compares amino acid sequences. This software also color-codes the amino acids based on their property. It can also generate a phylogenetic tree for the sequences inputted (I used Clustal Omega to construct the Pham 72026 phylogenetic tree that can be seen on my poster).
Thank you very much! The reason I picked the second domain over the first is because the second domain is found in various phage and bacterial genomes. When you see a gene found in both phage and bacteria, it is a good indication that horizontal gene transfer might have played a role. My research goal was to see if I can find evidence on how Auspice was able to acquire the gene (through vertical inheritance or horizontal gene transfer). Therefore, I have chosen the second domain instead of the first.
The grouping of the different phage groups indicate that those phages are closely related. When we are trying to detect horizontal gene transfer, we would expect to see phages with no relation to be grouped together – we wouldn’t see a pattern. In the pham 72026 phylogenetic, we see a clear pattern where phages that infect the same host genus are grouped together. This pattern suggests that the inheritance of this gene is likely due to vertical gene transfer (inheritance of genes from the parent).
Yes, a singleton is not a cluster. Phages are grouped into clusters based on their genomic similarity, and when a phage does not show any genomic similarity to an already established cluster, it is referred to as a singleton.
Does Cluster Omega software do anything other then find the representative phage?
Thank you for your question! Clustal Omega is a software that aligns and compares amino acid sequences. This software also color-codes the amino acids based on their property. It can also generate a phylogenetic tree for the sequences inputted (I used Clustal Omega to construct the Pham 72026 phylogenetic tree that can be seen on my poster).
Hi Sahithi, great job. Is there any reason you picked the second domain rather than the first?
Thank you very much! The reason I picked the second domain over the first is because the second domain is found in various phage and bacterial genomes. When you see a gene found in both phage and bacteria, it is a good indication that horizontal gene transfer might have played a role. My research goal was to see if I can find evidence on how Auspice was able to acquire the gene (through vertical inheritance or horizontal gene transfer). Therefore, I have chosen the second domain instead of the first.
What does the grouping of each of the different phage groups in the phylogenic tree mean?
The grouping of the different phage groups indicate that those phages are closely related. When we are trying to detect horizontal gene transfer, we would expect to see phages with no relation to be grouped together – we wouldn’t see a pattern. In the pham 72026 phylogenetic, we see a clear pattern where phages that infect the same host genus are grouped together. This pattern suggests that the inheritance of this gene is likely due to vertical gene transfer (inheritance of genes from the parent).
Is singleton not a cluster?
Yes, a singleton is not a cluster. Phages are grouped into clusters based on their genomic similarity, and when a phage does not show any genomic similarity to an already established cluster, it is referred to as a singleton.