Contents

• Contents
• PepPepSearch: searching SwissProt for a peptide sequence
  • Usage
  • Examples
  • Restrictions and common problems
  • Related Darwin functions
  • Methods
    • Finding candidates
    • PAM estimation and final selection
• AllAll: Related peptide sequences
  • Usage
    • Sequence specification
    • Commands
  • Examples
  • Restrictions and common problems
  • Related Darwin functions
  • Methods and applications
    • Tree construction
    • Multiple alignment and probabilistic ancestral sequence
    • Structure prediction according the E.T.H. method
• AllAllDB: querying the all-against-all database of SwissProt
  • Usage
  • Examples
  • Restrictions and common problems
  • Related Darwin functions
  • Methods
• MassSearch: searching SwissProt or EMBL by protein mass after digestion
  • Usage
  • Examples
  • Restrictions and common problems
  • Related Darwin functions
  • Methods
• NuclPepSearch: searching SwissProt for a nucleotide sequence
  • Usage
  • Examples
  • Restrictions and common problems
  • Related Darwin functions
  • Methods
    • Finding candidates
    • Nucleotide peptide alignment
    • PAM estimation and final selection
• TreeGen: tree generation from distance data
  • Usage
  • Examples
  • Related Darwin functions
  • Methods
• Darwin: running the Darwin tool
  • Usage
  • Examples
  • Restrictions and common problems
• PredictGenes: predict and verify gene structure by alignment with homologous proteins
  • Usage
  • Examples
  • Restrictions and common problems
  • Related Darwin functions
  • Methods
• Amino acids, bases, and similarity scores
• Amino acids
• Bases
• Genetic code
• Amino acid similarity matrix at 250 PAM
• Peptide gap penalties
• References