tutorials:eccb_t2_badasp
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| Both sides previous revisionPrevious revisionNext revision | Previous revision | ||
| 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 " | ||
| - | < | ||
| - | cd ./ | ||
| - | </ | ||
| Execute **badasp** by importing the multiple alignment in FASTA format (" | Execute **badasp** by importing the multiple alignment in FASTA format (" | ||
| - | < | + | |
| + | < | ||
| + | cd ./ | ||
| + | python badasp.py seqin=badasp_eg.fas i=1</ | ||
| Badasp will ask for the associated tree, in newick format (" | Badasp will ask for the associated tree, in newick format (" | ||
| 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. | => Press M, then enter. | ||
| (Tree displayed) | (Tree displayed) | ||
| - | Choice? [default=Q]: | + | Choice? [default=Q]: |
| Node [default=0]: | Node [default=0]: | ||
| => Type VPP1, then Press enter | => Type VPP1, then Press enter | ||
| - | Choice? [default=Q]: | + | Choice? [default=Q]: |
| Node [default=0]: | Node [default=0]: | ||
| => Type VPP4, then Press enter | => Type VPP4, then Press enter | ||
tutorials/eccb_t2_badasp.1347117975.txt.gz · Last modified: by romainstuder
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