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Cutting Edge Project - Tree of Life
Posted: Sat Oct 23, 2004 12:27 pm
by bshwckr593
Hello, I am doing the "Using Protein Sequences to Infer Relationships in the Tree of Life" project. After I align the sequences, what information do I input into a data table? And how should this data table be set up? My results are
http://www.ebi.ac.uk/cgi-bin/clustalw/r ... 4&poll=yes
Posted: Wed Oct 27, 2004 4:39 pm
by shijun
Hi,
Did you read the section: "Tips for Formatting Sequences?" Also pay attention to this part of the instructions: "This comparison is done by making an "alignment" of all of the proteins you are comparing and then "counting" the differences. Do the relationships shown in your tree agree with where your animals appear on the old tree? Can you think of an explanation for whatever outcome you get?"
Can you come up with some ideas?
BTW, I couldn't access the link you posted.
Shijun
Science Buddies Staff
Still need help
Posted: Sat Oct 30, 2004 3:59 pm
by bshwckr593
Thanks for all the help, shijun. However, I created a "blosum" matrix from the data. However, it is not clear to me how the various 'scores' are calculated. Here it is:
7
gi|15341650|ref|NP_203506.1| 0.000 0.965 0.916 0.898 0.977 0.945 0.922
gi|49146562|ref|YP_026070.1| 0.965 0.000 0.957 0.953 0.898 0.953 0.957
gi|26983978|gb|AAN77596.1| 0.916 0.957 0.000 0.928 0.975 0.912 0.237
gi|5835192|ref|NP_008238.1|COX 0.898 0.953 0.928 0.000 0.969 0.922 0.926
gi|33943837|gb|AAQ55579.1| 0.977 0.898 0.975 0.969 0.000 0.977 0.969
gi|5834880|ref|NP_006949.1|COX 0.945 0.953 0.912 0.922 0.977 0.000 0.906
gi|5834900|ref|NP_006967.1|COX 0.922 0.957 0.237 0.926 0.969 0.906 0.000
What do the numbers mean? I understand that they are comparing each individual sequence to another, but where do they get those numbers. Thanks again. [/img]