ngoto-biotree-public.ppt

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1 BioRuby

2 : 719 : GenBank, EMBL, DDBJ, PDB, KEGG, Galperin, M.Y. (2005) The Molecular Biology Database Collection: 2005 update. Nucleic Acids Research, 33: D5-D24. : : BLAST, FASTA, CLUSTAL W, Bioinformatics

3 : 968 : GenBank, EMBL, DDBJ, PDB, KEGG, Galperin, M.Y. (2007) The Molecular Biology Database Collection: 2007 update. Nucleic Acids Research, 35: D3-D4. : : BLAST, FASTA, CLUSTAL W, Bioinformatics

4 : 968 :

5 ~ : : BLAST CLUSTAL W : : BLASTe-value e-value0.1a B

6 BioRuby Ruby

7 Ruby : Perl Java

8 Perl Java Python BioPerl BioJava Biopython Open Bioinformatics Foundation (OBF) (OBDA)

9 Ruby

10 BioRuby bioruby.org/

11 BioRuby 2000/11/21 BioRuby Ruby 2001/06/ , 20 20, / /02 IPA 2006/02/ /12/ pre pre pre1 : 173 : 38, : bioruby.org/

12 Newick New Hampshire (((mouse:0.04, rat:0.05):0.12, (horse:0.10, cow:0.14):0.02):0.05, human:0.08); mouse rat horse cow human 0.05

13 Newick root root (Graph) (Graph) root root (((mouse:0.04, rat:0.05):0.12, (horse:0.10, cow:0.14):0.02):0.05, human:0.08); human horse mouse cow rat 0.05

14 Bio::Tree + Bio::Pathway Bio::Pathway BioRuby Bio::Pathway Bio::Pathway Ruby Ruby Boost Graph Library

15 Bio::Tree Newick root root Daniel Amelang BioRuby Newick root root

16 Bio::Tree #!/usr/bin/env ruby require 'bio' str = '(((mouse:0.04, rat:0.05):0.12, (horse:0.10, cow:0.14):0.02):0.05, human:0.08);' # Newick newick = Bio::Newick.new(str) # Bio::Tree tree = newick.tree # Array Array p tree.nodes # (leaf) (leaf)array p tree.leaves # (edge) (edge)array p tree.edges

17 Bio::Tree Bio::Tree Bio::Tree::Node Bio::Tree::NodeBio::Tree::Edge Bio::Tree::Node (leaf) (leaf) root Bio::Tree::Edge (edge) (edge)

18 (root) (root) #!/usr/bin/env ruby require 'bio' str = '(((mouse:0.04, rat:0.05):0.12, (horse:0.10, cow:0.14):0.02):0.05, human:0.08);' tree = Bio::Newick.new(str).tree # root root p tree.root # mouse mouse = tree.get_node_by_name('mouse') ') # mouse p tree.ancestors(mouse) # horse cow horse = tree.get_node_by_name('horse') ') cow = tree.get_node_by_name('cow') ') # horsecow cowroot tree.root = tree.lowest_common_ancestor(horse,, cow) # mouse p tree.ancestors(mouse) # Newick print tree.output_newick

19 Bio::Tree each_node each_edge adjacent_nodes(node) node out_edges(node) node add_node(node) node node remove_node(node) node add_edge(node1, node2, edge) node1node2 node2edge remove_edge(node1, node2) node1node2 node2 distance(node1, node2) node1node2 node2 path(node1, node2) node1node2 node2 parent(node) node children(node) node descendents(node) node leaves(node) node distance_matrix adjacency_matrix subtree([ node1, node2,...]) subtree remove_nonsense_nodes : tree(network)

20 --- Deep copy Ruby Ruby PhyloXML Phylip, Molphy,, PAUP, Hyphy

21 BioRuby bioruby.org/ ChemRuby chemruby.org/ bio.jp/ bioinformatics-jp

22 Phyloinformatics Hackathon 2006/12/10-15 NESCent National Evolutionary Synthesis Center Durham Duke

23 Phyloinformatics Hackathon

20110325-ob14-ktym-revised.key

20110325-ob14-ktym-revised.key BioRuby 10 http://bioruby.org/ 46th SIG-MBI / 14th Open Bio 2011/3/25-26 @ JAIST 2000 BioPerl KEGG, GenBank Perl BioPerl BioPerl Ruby BioRuby 2000 2001 BOSC - Bioinformatics Open Source