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tutorials:eccb_t2_badasp [2012/09/07 15:46]
romainstuder 		tutorials:eccb_t2_badasp [2012/09/08 16:15] (current)
romainstuder
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 ==== BADASP ==== ==== BADASP ====
  
-BADASP can produce different kind of measure:+BADASP can produce different measures:
  
    * bad: similar the **Type II** of functional divergence. The threshold to choose depend if we want to be stringeant (i.e. BAD > 4) or more relaxed (BAD > 2).    * bad: similar the **Type II** of functional divergence. The threshold to choose depend if we want to be stringeant (i.e. BAD > 4) or more relaxed (BAD > 2).
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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"):
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 => Press enter => Press enter
 +</code>
 Display Tree, with two groups of sequences: Display Tree, with two groups of sequences:
 V-type proton ATPase 116 kDa subunit a V-type proton ATPase 116 kDa subunit a
-- VPP1 = VPP Isoform 1 (8 genes) +   * VPP1 = VPP Isoform 1 (8 genes) 
-- NVL = VPP Isoform 4 (3 genes) +   * NVL = VPP Isoform 4 (3 genes) 
 +<code>
 Rooted Tree (1000 bootstraps). Branch Lengths given. 21 nodes.  <ENTER> to continue. Rooted Tree (1000 bootstraps). Branch Lengths given. 21 nodes.  <ENTER> to continue.
 => Press enter => Press enter
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 => 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
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 </code> </code>
  
-Badasp will now perform some computation. It will reconstruct the ancestral sequences at each node of the tree, using the [[http:dx.doi.org/10.1186/1471-2105-5-123|GASP (Gapped Ancestral Sequence Prediction) method]]: +Badasp will now perform some computations. It will reconstruct the ancestral sequences at each node of the tree, using GASP (ref: http:dx.doi.org/10.1186/1471-2105-5-123 )
  
 +<code>
 Making Ancestral Sequences - Variable PAM Weighting Making Ancestral Sequences - Variable PAM Weighting
 Reading PAM1 matrix from jones.pam Reading PAM1 matrix from jones.pam

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