NCBI Data Mining Tools: NCBI Genome Workbench

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NCBI Data Mining Tools NCBI Genome Workbench

• http//www.ncbi.nlm.nih.gov/projects/gbench/

June 10, 2008
Ceske Budejovice, Czech Republic
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Tools for Data Mining at NCBI
Nucleotide Sequence Analysis
Structures
Protein Sequence Analysis and Proteomics
Genome Analysis
Gene Expression
http//www.ncbi.nlm.nih.gov/Tools/
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Tools for Data Mining at NCBI
Nucleotide Sequence Analysis
Structures
Protein Sequence Analysis and Proteomics
Genome Analysis
Gene Expression
http//www.ncbi.nlm.nih.gov/Tools/
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Genome WorkbencH

• What it is?
• Provide an interactive, client side GUI
• Provide a suite of annotation tools
• Provide a platform for visualization and analysis
• Provide an easily extensible platform
• View data from publicly available sequence
  databases, e.g. NCBI and your own private data.
• Display sequence data as
• graphical sequence views, various alignment
  views, phylogenetic tree views, and tabular views
  of data.
• Align your private data to data in public
  databases, display your data in the context of
  public data, and retrieve BLAST results.

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Genome Workbench Home Page
http//www.ncbi.nlm.nih.gov/projects/gbench/
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Genome Workbench All Screens
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Workspace vs Project

• Projects Hold Data. Workspaces Hold Projects. It
  is best to combine data that go together inside
  projects, and to use workspaces to hold
  collections of projects that may or may not go
  together.

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Project Tree

• The Project Tree is a view on your workspace and
  projects. The project tree shows you a
  hierarchical expansion of your data, and allows
  you to group data items into folders.
• The Project Tree is available from the main menu
  at View -gt Project Tree. It is on by default, and
  appears on the left-hand side.

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Tools Selection Inspector

• The selection inspector provides a means for
  evaluating all the selected objects in Genome
  Workbench.
• The selection inspector has three modes of
  operation (Table, Brief Text, and Full Text),
  selectable by using the icons in the right-hand
  corner of the view
• Aggregating selection across views
• Show selection from all view

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Data Mining View

• The data mining view is a view that combines many
  modes of searching into one interface. From the
  data mining view, you can search for items in the
  public sequence repository you can search for
  gene records from Entrez Gene you can search for
  annotations in a given view and you can search
  for patterns of sequences.
• The data mining view is on by default, and is
  available from View -gt Data Mining View. It is
  generally docked along the bottom

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Supported Data Formats

• FASTA sequence files
• GFF2/GTF format (NOTE GFF3 support will be added
  soon)
• RepeatMasker .out format
• Sequin-style 5-Column Feature Table format
• Newick-format phylogenetic trees
• Phrap/ACE assembly files
• AGP sequence assembly files
• NCBI ASN.1 objects (in ASN.1 text or binary or in
  XML format)
• NOT GenBank nor EMBL Flatfile format

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Manage/Add Plug-ins
Plug-ins developed in Python (best support) and
PerlMaybe too cluttered to load everything
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Tools Alignment
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Tools Composition
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Tools Phylogenetic Trees
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Tools Send to Web Pages
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Example
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Example 2
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Genome Workbench Screenshots
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Streptococcus pyogenes Alignments Using Genome
Workbench

• Workspace containing ONE project that shows the
  relationship of two bacterial genomes, both
  serotyped as Streptococcus pyogenes strains. The
  alignments are notable for two large inversions
• This project includes an alignment of
  Streptococcus pyogenes (serotype M3, strain
  SSI-1, NC_004606 ) to Streptococcus pyogenes
  (serotype M6, strain MGAS10394, NC_006086 ).

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Streptococcus pyogenes Alignments
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Streptococcus pyogenes Alignments
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Streptococcus pyogenes Alignments
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Streptococcus pyogenes Alignments