Help interpreting BLASTn results and phylogenetic tree for genetics practical

Question

[simonlydialm]

Hi everyone,

I'm working on a genetics practical where I used BLASTn to analyze a DNA sequence. I’ve run the search on NCBI and now need help interpreting the results for my report. Specifically, I’m looking for guidance on:

Identifying the organism from the top hit

Understanding the % identity and what it implies

Interpreting the alignment from the second hit

Generating and analyzing a Fast Minimum Evolution phylogenetic tree (first 10 hits vs. last 10 hits)

Inferring evolutionary relationships from the tree

Exploring protein homology from the third hit and predicting gene function

If anyone can help me walk through these steps or explain how to interpret the tree and protein products, I’d be super grateful. I’m aiming to write a clear, referenced report and want to make sure I understand the bioinformatics properly.

Thanks in advance!

Answer 1

[Mensur Dlakic]

I think what you are asking involves too much work for anyone to explain it in granular detail. But who knows, maybe there is a good soul out there who is willing to do it.

I will briefly address some of your questions. When you get BLAST hits, assuming this is done on the web, on the far right side there is a column titled Accession. If you open that in a new window, within the top 10 lines you will have an organism name listed. If you are doing this locally, again there will be accession numbers that can be used for an NCBI search to find organism names.

What exactly are you unclear about percent identity? Broadly speaking, more related proteins means that their corresponding organisms are also more related. Pick pretty much any human protein and BLAST it, and you will find that a related chimpanzee protein will be 98-99% identical, a similar mouse protein might be 95% identical, and a chicken protein might be 90% identical. These are not real numbers and won't apply across the board, but rather an illustration that we are more related to chimps than mice, and to mice more than birds.