PRESTO

PRESTO is an extended version of the parts of the program INTERCHEM which handle protein and nucleic acid sequence information, and which do not involve display of 3D structural data.

The three main functions in the program and the various individual operations are:-

• Aligning peptide and protein sequences
  • Up to 200 sequences each of 800 amino acid residues can be handled
  • Entry of single or multiple sequences in either 1 or 3 character codes
  • Loading of series of sequences stored in a previous session
  • Editing functions
    • Insertion of residues and gaps
    • Deletion of residue or gap
    • Deletion of blocks of residues
    • Insertion of columns of gaps
  • Deletion of single or set of contiguous sequences
  • Copying and moving of single and sets of contiguous sequnces
  • Storing of single or sets of sequences in files
  • Aligning of sequences
    • Pairwise alignment
    • Alignment of sets of sequences
    • Choice of eleven similarity matrices
    • Scramble sequence
    • Reverse sequence
  • Examine evolutionary trends in a set of aligned sequences by covariation analysis
  • Form dendrogram from set of aligned sequences
    
• Prediction of secondary structure of peptide sequences
  • Choice of four popular predictive methods
  • Manual editing of predictions
  • Formation of torsional angle file for use in peptide building in INTERCHEM
    
• Translation of nucleic acid sequences into peptide/protein sequences
  • Reading in of DNA or RNA sequences
  • Display of current sequence
  • Translation to amino acid sequence using 3 reading frames
  • Survey mode translation using each reading frame in turn
  • Form complementary strand
    
• An image of the display screen in the form of an "rgb" file may be made at any stage, so that data may be transfered to (for example) the standard SGI program SHOWCASE .

Reference to novel techniques used in PRESTO:

• Rapid alignment of Sequences: Peter Bladon. J. Chem. Inf. Comput Sci., 2001, 41, 278-280.
• Covariation Analysis. Leighton Pritchard, Peter Bladon, Jane Mitchell, and Mark. J. Dufton. Protein Engineering, 2001, in the press.

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Revised 18th June 2007