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\begin_layout Title
Breadcrumb trail to exciting new free data!
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\begin_layout Author
Thomas E.
 Keller
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\begin_layout Abstract
I've mentioned to a few people that I was working on an Actin protein family
 protein problem.
 If you have no idea what I'm talking about, look up the wikipedia article
 on Actin.
 At the end of the analysis pipeline I performed are two different trees,
 a RAxML maximum likelihood tree of the protein phylogeny, and a MrBayes
 95% consensus tree of the DNA sequences.
 I'll just state that my opinion is that there are some very interesting
 questions to explore, so we should all get our hands dirty and start mucking
 around with the data and develop new ways of exploring it.
 I encourage everyone to play with the python code I developed, and think
 about what was annoying about it and possible ways to make it better and
 more general.
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\begin_layout Section*
The light at the end of the tunnel
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\begin_layout Standard
Along with this document there is a python file that will download a bunch
 of sequences and generate a fasta file.
 The sequences I was interested in happen to be from the actin family.
 They are known to be extremely conserved, such that though they exist in
 pretty much all eukaryotes, the size of different protein groups only varies
 by a few amino acids, and most of the amino acids themselves are the same.
 I think they are all about 80% similar or more.
 But what does the DNA sequence phylogeny look like? Does it reflect the
 same patterns, or suggest something different?
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Figure out how to download and use Figtree to look at the trees.
 Don't be afraid of feeling overwhelmed; it's a lot of data.
 Try zooming in and moving around various parts of the tree and explore
 the different patterns.
 
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I'd look at the amino acid tree first.
 The huge polytomies indicate that indeed, most sequences within a protein
 sub-group are identical at the amino acid level.
 But one group, the Beta-like actin family, seems to be evolving relatively
 rapidly compared to the rest of the groups.
 I wonder what it's dn/ds ratio is?
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The terms Alpha, Beta, and Gamma reflect the historical fact that these
 broad groups of proteins spread at approximately the same rate.
 But do the two Gamma types seem to be sister protein sub-families?
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\begin_layout Section*
Now start at the beginning
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The first python script downloads all actin sub-families and creates a fasta
 file where each line of a text file is the combined name of the estimated
 human-vertebrate ortholog, and the vertebrate common name.
 However, the dataset that produces takes some time to run properly in RAxML
 and MrBayes right now.
 I'd pick a part of the phylogenetic tree and start with a protein subfamily
 (get the single yeast gene as well so you can root the tree (since you
 know the answer in advance is that it's the outgroup of vertebrate actins).
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\begin_layout Standard
Take a look at the python script, don't just run it.
 How could it be made better and more general? There are some pretty easy
 things that would vastly improve it.
 For instance, I assumed that I wanted to only download Actin stuff; with
 only a little bit of extra code it could be made to do the same thing for
 any gene family.
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\begin_layout Section*
What next?
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\begin_layout Standard
Well, the next thing I did was download the most recent sate program.
 It apparently assumes some things that make it inconvenient to run on a
 cluster, but run it for awhile on your personal pc.
 Take a look at the aligned output in some free alignment viewer.
 I went with Jalview, though it has several annoying defaults, like just
 dumping you to the sequences with no color information.
 Also it starts up with annoying bells and whistles until you figure out
 how to turn those off.
 What stands out to you? Can you think of how to write a program that would
 clean up some of the weirdness?
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\begin_layout Standard
There's already plenty of weird stuff going on, and we haven't even to the
 amino acid alignments or any phylogeny estimation (aside from what sate
 produces).
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\begin_layout Section*
Write up what you found out and got excited about!
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\begin_layout Standard
Work on this for up to a day.
 Relax, and come back the next morning.
 What parts did you like? Where did you get frustrated? Where did you wish
 there was more clear documentation to find out what to do next? What did
 you like and dislike about the various programs being used? Is there a
 public access repository for data and program files that are not associated
 with a published paper?
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