BLAST into the past: Cynops sequence is now closer to T rex?

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BLAST into the past: Cynops sequence is now closer to T rex?

Postby punkrockewok » Fri Jan 24, 2014 12:38 pm

I am measuring what animal has BLAST protein sequences that measure most closely with the T.Rex protein sequence.

I followed the directions on this site, but the results and the mapping now make it look like the Firebelly Newt is more closely related than the chick. That goes against all the articles and the directions, so I don't know what I'm doing wrong. The overall Identity % and the overall score is higher for the Newt. The only things higher for the chick are the "max score," and the e value is WAY smaller, but they are all so small I don't know how much that counts (they are all smaller than the recommended 1e-6).

And when I ask it to map (following the directions, and also trying different mapping options) it shows the Newt as closer than the chick.

Help! Am I reading this right? Are their more sequences available so the amphibian is now shown as being closely related to the reptile and that's ok? But the chick is still close so still a close relative?

THank you!
-Collette
punkrockewok
 
Posts: 3
Joined: Fri Jan 24, 2014 12:19 pm
Occupation: student 5th
Project Question: T Rex's Closest Living Relative (BLAST into the past)
Project Due Date: February 3.
Project Status: I am finished with my experiment and analyzing the data

Re: BLAST into the past: Cynops sequence is now closer to T

Postby punkrockewok » Fri Jan 24, 2014 4:34 pm

I found a .doc assignment using the same procedure that says to only use the Max score and the E value (http://blossoms.mit.edu/sites/default/f ... andout.pdf).

I will go with this explanation. But it still doesn't explain why the graphics for this science project don't work anymore on BLAST. I still need to find a workaround for that. Anyway, FYI.
punkrockewok
 
Posts: 3
Joined: Fri Jan 24, 2014 12:19 pm
Occupation: student 5th
Project Question: T Rex's Closest Living Relative (BLAST into the past)
Project Due Date: February 3.
Project Status: I am finished with my experiment and analyzing the data

Re: BLAST into the past: Cynops sequence is now closer to T

Postby heatherL » Thu Jan 30, 2014 7:03 am

Hi Collette,

This is a really interesting project, and it sounds like you have done your research.

Keep in mind that the relationships you find will depend a lot on which protein you compare. There may be some proteins that are more derived in the chick, which will cause it to separate out from the T. rex and the newt. Can you share a bit more about which proteins you compared?

Heather
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Project Question: How do different animals adapt to their environment?
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