Acquiring Sequences

My mentor was in San Diego this week, so I worked through Chapter 4: Acquiring Sequences of the book Phylogenetic Trees Made Easy on my own.

The most time-consuming part of estimating a phylogenetic tree is acquiring the sequences that will be the tips of the tree. Today, I learned how to find related sequences, and what criteria I should consider as I decide which sequences to include. The BLAST search in the MEGA program is the primary tool for identifying sequences that are homologous to your sequence of interest, the query sequence, and I used it today to acquire sequences related to the E. Coli bacteria.

Here is a screenshot of all the DNA sequences I acquired in BLAST:

It took me some time to figure out how to correctly acquire sequences. When you enter the query sequence, BLAST pulls up all the related DNA sequences, but it's up to you to determine which results will actually be useful. Then, you have to click on each sequence of interest and go through a process in which you add the sequence to your list in the correct format. Since the book was written for an earlier version of MEGA than the one I have, it took a lot of trial and error to correctly acquire all the sequences.

Phylogenetic Trees

This week, I started learning phylogenetic analysis, which biologists use to understand evolutionary and molecular relationships. Dr. Miller gave me a book called "Phylogenetic Trees Made Easy," and I completed the first tutorial in it, which outlined the steps for creating a simple phylogenetic tree.

To make the tree, I first had to download a program called MEGA 5, which analyzes and aligns sequences from related organisms. Specifically, I looked at a sequence from the bacterium Thermotoga petrophila. I used a "search engine" called BLAST to help me find sequences that produced similar alignments to the original sequence. I chose the 6 most closely related sequences, and then used the program to produce a DNA alignment:

The final step, which was to construct a phylogenetic tree based on the alignment, was actually pretty simple. All I did was click on a button labelled "Neighbor Joining Tree," and the program created a phylogenetic tree for me! Getting the alignments was the hard part, because it's so easy to make simple mistakes, which can mess up the whole alignment. It took Dr. Miller and me several tries to get it right. 

Phylogenetic tree!

Internship Revealed!

My STEM internship for 2014-2015 is (drumroll, please)... evolutionary biology with Dr. Mark Miller! Dr. Miller is currently working on a research project called Next Generation Tools for Biology at the San Diego Supercomputer Center (he commutes to Albany each week). He develops software tools and infrastructure for biomedical applications. This internship is perfect for me, because I can build on the programming skills I learned last year but also explore the field of evolutionary biology.

I don't know yet what research problem we'll be working on-- right now, I'll just be learning the basics of creating phylogenetic trees with him. We'll start on a research project next semester. Last year, Peggy and Dr. Miller worked on a project with the San Diego Zoo to trace the origins of a disease affecting a species of birds there. It was really cool and I look forward to what I'll be doing!