Vector NTI

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Vector NTI

• Molecule (DNA, protein, genome) display
• Restriction analyses
• Primer design
• Cloning strategies
• Gel display
• Analyses with other modules

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Vector NTI window
Graphic pane
Text pane
Sequence pane
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Open a molecule
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Display text pane (DNA molecule)
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Display text pane (protein)
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Tool bars
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DNA Molecule display setup
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Protein display setup
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Display of a protein motif
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Set a selection
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Display of selection
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Select a feature
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Selected display
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Display of a selected fragment (1)
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Display of a selected fragment (2)
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Edit a molecule
Right click
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Modify the sequence
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Discard modifications
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Insert a sequence
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Modify a feature
Right click
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Add a feature
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Change start coordinate
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Create an internal numbering
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Find an object from the text pane
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Find a sequence
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Graphic display setup
Right click
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Save display setup
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Edit the graphic (1)
Right click
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Edit the graphic (2)
Right click
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Save a molecule
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Other tools
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Restriction analysis
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RFLP
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Common non cutter
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Mutagenesis
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ORF display (1)
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ORF display (2)
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Vector NTI options
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Primer design
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Find primers
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Analyze and save
Right click
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Look for oligo duplexes
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Save PCR product
Right click
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Display amplicons
Right click
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Find sequencing primers
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Find hybridization probe
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Multiplex PCR
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Exercise 2

• Open pBR322
• Change display to linear and use zooms
• Modify TCr display (color, size, text)
• Display one strand
• Select sequence 100-1000, translate both strands
• Design PCR primers (modify parameters)
• Save PCR analysis, display onto molecule

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Exercise 3

• Open FYN
• Localize N-glycosylation and C-mannosylation
  sites
• 100 similarity
• Select and display 149-231 in a new window.

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BioAnnotator
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Biochemical analyses of protein
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Biochemical analyses of DNA fragment
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Analysis Monitor
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Protein analyses
Not working in demo mode
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BLAST search
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Blast output
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Analysis of blast hits
Right click
Right click
Right click
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AlignX
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Select molecules to align
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Analyses of aligned protein sequences
Right click
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Analyses of aligned nucleotide sequences
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Alignment setup
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Comparison tables
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Display set up and dot matrix
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Alignment and primer design
Right click
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Display molecule features on alignment
Right click
Right click
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Exercise 4

• Align nucleotide sequences from pATH1, pATH2,
  pATH21 and pATH23
• Do the same alignment using pATH1 as first
  profile (note the difference in the consensus at
  around position 1390)
• Design primers for region 1200-1600
• Save PCR products and display with vectorNTI

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Exercise 5

• Open protein.apr (demo projects)
• Display features from PCNA-orysa.