GenomBench

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GenomBench
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Open a molecule
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Load a fragment
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Loading monitor
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Fragment display
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Display options
Double click
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Mark a segment
Right click
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Mark a feature
Right click
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Navigate through marks
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Display option feature by position
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Display option small representation
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Edit a feature
Right click
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Group selected features
Right click
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Display sequence of loaded fragment
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Alignment
drag
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Feature linked to a sequence
Right click
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Translate selection
Right click
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Translate marks
Right click
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Display information about loaded fragment
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Customize feature table
Right click
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History, feature filter
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Display options
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Display configuration
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Feature search
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Pattern search
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Send features to vectorNTI
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Sim4 mapping
Right click
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Spidey mapping
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Genombench query application
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Query a genome browser
Right click
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Exercise 7

• Open UCSC mar 2006 fragment 1
• Load 1 000 000 nucl. from position 100 000 000.
• Find EST BI831763
• Mark feature (all exons)
• Translate marks on both strands.
• Group ESTs BI831763, BI561833 and DB022932.
• Align to genomic sequence
• Find and create features for ATCGATGA

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Exercise 8

• Use query application to search for receptor
  tyrosine kinase in fruitfly in the UCSC genome
  browser.
• Display the Chromosome X hit in GenomBench

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3D Molecule Viewer
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3D molecule display
Right click
Right click
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3D molecule display setup
Right click
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3D options
Right click
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Align chain
Align backbone mode
Right click
Align atoms mode
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Calculate surface
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Other functionalities

• Shared databases (user manual, page 383)
• GCG Converter (user manual, page 643)
• Matrix Editor (user manual, page 646)
• Customization (user manual, page 625)

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Exercise 9

• Use Pubmed/entrez to search for structures of HIV
  Gp120
• Open structure 44088 (2NY7)
• Mark Chain L
• Modify display (zoom, rotation)
• Select structure 44083 (2NY2), export to file
• Align chainA of 2NY2 with chainG of 2NY7
• Calculate surface for 2NY7 using Conolly method