Contents

• Contents
• What is SCANPS?
• Principal features of SCANPS
• Availability
• Disclaimer
• Citing SCANPS
• How to use SCANPS to search a protein database
  • Introduction
    • Introduction to Unix Pipes and redirection
  • Simple Scanning - just returns top score for each sequence
    • Scan with sequence using default parameters and database
    • Sort the result
    • Examine the hit list
    • Extracting the sequences from the database
    • Generating the local alignments
    • Generating the local alignments - estimating significance
  • Advanced Scanning - apply the NALL algorithm to the database
    • Introduction
    • Running the NALL scan
    • Running sortsco to sort the output and get titles
    • Processing the results of the NALL scan
    • Further analysis of the NALL output
• Scanning with an Alignment
• Comparing all pairs of sequences
• Cluster analysis with program ``oc''
  • Other functions of program oc
• How to build an indexed database for use with scanps
• Installation of scanps, sortsco, select, id_pir3and simclean
• Example database
• Hints and tips for successful searching
• File formats
  • Sequence file format
  • Multiple alignment query format
  • Matrix File format
  • Defaults file format
  • Command line options
• References
• About this document ...