PepTool

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PepTool

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

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PEPTOOLS LAUNCHER BAR
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DATA FLOW FOR PEPTOOLS
Ways to insert data into the program
Ways to edit your data if it is not in the
correct format
Ways to analyze your data
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• File Types Supported
• PIR
• Swiss-Prot
• Pep Tool
• GCG
• Intelligenetics
• Structure DB
• BLAST
• FASTA
• SEQSEE
• RAW
• Text

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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-Showing Structure
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SEARCH TOOLS

• Search Options
• By Homology
• By Keyword
• By Pattern
• By Sub-sequence

• Search Locations
• BioTools Database
• Structure DB

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Keyword Search
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Output for a Keyword Search
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Search by Homology Results
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ANALYSIS TOOLS

• Analyze
• Predict Structures
• Protein Statistics
• Find Motifs

• Graph
• Hydrophobicity
• Helix Hydrophobic Moment
• Beta Hydrophobic Moment
• Flexibility
• Dot Plot
• Helical Wheel

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Predict Structure
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Find Motifs
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Find Motifs-Graphical View
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Protein Statistics
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Dot Plot
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Helical Wheel
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Graph Output (Beta Hydrophobic Moment)
Note-Hydrophobicity, Helix Hydrophobic Moment,
Beta Hydrophobic Moment and Flexibility all have
the same graphical output windows.
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• Analysis Tools
• Alignment of proteins using the XALIGN algorithm
• Heuristic analysis

• Display Tools
• Color by Structure
• Color by Property
• Color by Identity
• Comparison Matrix

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Alignment Editor-Showing Conserved Regions
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SummaryWhat can you do with PepTool?

• Determine Hydrophobicity

• Determine beta and helix hydrophobic moments

• Look for homologous sequences

• Align sequences to determine regions of consensus

• Find repeats and motifs

• Determine protein secondary structure