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tutorials:eccb_t2_badasp [2012/09/08 15:26] romainstuder |
tutorials:eccb_t2_badasp [2012/09/08 16:15] (current) romainstuder |
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We want to identify the residues making differences between the **isoforms 1** and **isoforms 4** of the V-type proton ATPase 116 kDa subunit a. | We want to identify the residues making differences between the **isoforms 1** and **isoforms 4** of the V-type proton ATPase 116 kDa subunit a. | ||
+ | First, visualise briefly the multiple alignment in Jalview. (File "badasp_eg.fas" in the badasp folder. | ||
- | <code> | ||
- | cd ./badasp # Folder of installation | ||
- | </code> | ||
Execute **badasp** by importing the multiple alignment in FASTA format ("badasp_eg.fas") and activating the interactive mode (i=1): | Execute **badasp** by importing the multiple alignment in FASTA format ("badasp_eg.fas") and activating the interactive mode (i=1): | ||
- | <code>python badasp.py seqin=badasp_eg.fas i=1</code> | + | |
+ | <code> | ||
+ | cd ./badasp # Folder of installation | ||
+ | python badasp.py seqin=badasp_eg.fas i=1</code> | ||
Badasp will ask for the associated tree, in newick format ("badasp_eg.nsf"): | Badasp will ask for the associated tree, in newick format ("badasp_eg.nsf"): | ||
Line 70: | Line 71: | ||
=> Press enter | => Press enter | ||
- | # We need to split the tree on the node 21, so we need to define two groups from the children nodes 20 (= VPP1 subfamily) and 19 (= VPP4 subfamily) . | + | # We need to split the tree on the node 21, |
+ | # so we need to define two groups from the children nodes 20 (= VPP1 subfamily) and 19 (= VPP4 subfamily) . | ||
=> Press M, then enter. # Manual grouping | => Press M, then enter. # Manual grouping | ||
(Tree displayed) | (Tree displayed) | ||
- | Choice? [default=Q]: c # We collapse node | + | Choice? [default=Q]: c # We collapse nodes |
Node [default=0]: 20 | Node [default=0]: 20 | ||
=> Type VPP1, then Press enter | => Type VPP1, then Press enter | ||
- | Choice? [default=Q]: c # We collapse node | + | Choice? [default=Q]: c # We collapse nodes |
Node [default=0]: 19 | Node [default=0]: 19 | ||
=> Type VPP4, then Press enter | => Type VPP4, then Press enter |