BioTools

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BioTools

• A Software Package for Analysis and Manipulation
  of Nucleic Acid and Protein Sequences

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GeneTool

• A Software Package for Analysis and Manipulation
  of Nucleic Acid Sequences

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GENETOOLS-TOOLBAR
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DATA FLOW FOR GENETOOLS
DATABASE
OPEN
SEARCH
TEXT
CHROMATOGRAM
EDITOR
EDITOR
MULTI-ALIGN
ASSEMBLY
SEQUENCE
EDITOR
EDITOR
EDITOR
Ways to insert data into the program
Ways to edit your specific data
Ways to analyze your data
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IMPORT TOOLS
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• REMOTE ENTREZ SEARCH OF GenBank DATABASE

GENETOOLS DATABASE
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Database Search
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Database Search Results
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• TYPE OF FILES SUPPORTED
• GenBank
• DDBJ
• EMBL
• dbEST
• dbSTS
• dbGSS
• FASTA
• ABI Chromatogram
• RAW (text)

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First Screen for Importing a Sequence (if not a
text file or a Gene Tools File)
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Second Screen for Importing a Sequence (if not
a text file or a Gene Tools File)
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DATA EDITORS
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• EDIT MENU
• Restore original Base
• Insert Base
• Find
• Find Next
• Find Next Problem
• Left/Right Trim

• VIEW MENU
• Vertical lines
• A Trace
• C Trace
• G Trace
• T Trace
• Reset Trace positions

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Chromatogram Editor
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• EDIT MENU
• Select all
• Find
• Cut
• Copy
• Paste

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Text Editor
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ANALYSIS TOOLS
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Sequence Editor
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VISUALIZATION TOOLS

• EDIT MENU
• Reverse
• Reverse Complement
• Circular sequence
• Set Origin
• Clear Features

• VIEW MENU
• Layout Sequence
• Double Stranded
• Translation
• Restriction Enzyme sites
• Features map
• Read back selection
• Set Group Size
• Uppercase

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Layout Sequence
Showing Restriction Sites, Double Stranded, and
Translation
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Feature Map
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ANALYSIS TOOLS

• ANALYZE MENU
• Translate
• Simulate Gel
• Compute Statistics
• Find Motifs, ORFs, Restriction Sites, Exons,
  Repeats and Vectors, PCR Primers
• FAST Alignment
• Remote BLAST

• PLOT MENU
• GC Density
• AT Density
• CpG Islands
• Ficketts Method
• Positional Bias

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Gel Simulation INPUT
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Gel Simulation OUTPUT
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Find Motifs
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Compute Statistics
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ORF Map
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Restriction Map
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Exon Map
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Find PCR Primers
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Plot Window
This window is the same for GC and AT content,
CpG islands, Ficketts Method, Positional Bias
and Codon Preference
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VISUALIZATION TOOLS

• EDIT MENU
• Find next problem
• Extend selection to start/end
• Add sequence
• Add Directory of Sequences
• Remove Sequence
• Sequence Information
• Consensus Threshold

• VIEW MENU
• Chromatogram
• Uppercase
• Color by
• Mismatch
• Identity
• Property
• Feature

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ANALYSIS TOOLS

• ANALYZE MENU
• Assemble
• Assembly Options
• Gap penalty
• Gap size penalty
• Identity strictness
• Minimum overlap

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Assembly Editor
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VISUALIZATION TOOLS

• EDIT MENU
• Extend selection to start/end
• Add sequence
• Add Directory of Sequences
• Remove Sequence
• Rearrange Sequences
• Sequence Information
• Consensus

• VIEW MENU
• Uppercase
• Color by
• Mismatch
• Identity
• Property
• Feature

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ANALYSIS TOOLS

• ANALYZE MENU
• Align all sequences
• Align selected region
• Pair wise identity matrix
• Align options
• Gap penalty
• Gap size penalty
• Rearrange by alignment

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Muli-Align Editor
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SummaryWhat can you do with GeneTool?

• Design primers

• Find restriction sites

• Help identify exons

• Map and simulate gels

• Assemble contigs

• Align sequences

• Find repeats, motifs and ORFs