PRESTO-PC

PRESTO-PC is a version of PRESTO adapted to work on Personal Computers running Microsoft Windows Operating Systems

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

• Aligning peptide and protein sequences
  • Up to 200 sequences each of 2100 amino acid residues can be handled
  • Entry of single or multiple sequences in either 1 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
    • Use of Needleman-Wunsch algorithm for global alignments
    • Use of Smith-Waterman algorithm for local alignments
    • Pairwise alignment
    • Alignment of sets of sequences using a very fast algorithm (1, 2)
    • Choice of twenty seven similarity matrices plus a user-defined matrix
    • Scramble sequence
    • Reverse sequence
  • Examine evolutionary trends in a set of aligned sequences by covariation analysis (3)
  • Form dendrogram from set of aligned sequences
  • An image of the display screen can be recorded in the form of a bit-map file at any stage
  • Program incorporates loading of sequences from, and searching of, locally held databases
    • PIR database
    • Swiss Prot database
    • PDB sequence database

References and footnotes:

• (1) Rapid alignment of Sequences: Peter Bladon. J. Chem. Inf. Comput Sci., 2001, 41, 278-280.
• (2) Time for global alignment of 29 sequences of average length 500 residues was 10 seconds
• (3) Covariation Analysis. Leighton Pritchard, Peter Bladon, Jane Mitchell, and Mark. J. Dufton. Protein Engineering, 2001, 14, 549.

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Revised 18th June 2007