RELEASE NOTES

FPS v2.0 -- June 9, 2000

• Added option of using GCG profiles as queries to FPS.
• Added command "blast2profile" for converting BLAST checkpoint files to GCG profiles. This command also supports replacing the truncated portions of the query sequence with the appropriate rows from a PAM or BLOSUM score matrix. Several such matrices are now included in the FPS distribution.
• Added option of using GCG profiles and BLAST checkpoint files as queries to the WEB version of FPS.
• Simplified the user interface to the "fps-all" command.
• Added the ability to use filters (such as seg) with the "fps-all" command to filter the queries before performing pairwise search.
• Added the "seg" command for filtering low-complexity regions from protein queries.
• Made filtering with "seg" the default for the WEB version of FPS and added switch to allow turning filtering off.
• Redesigned the "fps-all" command to facilitate adding new pairwise search methods.
• Added the "fps-swp" command to support using Smith-Waterman search on the Paracel Genematcher.

  FPS v1.0 -- March 11, 1999

• Initial release of FPS
  • fps: standalone version of FPS supporting three score combination functions:
    • POP (p-value of the product of p-values),
    • PMINP (p-value of the product of p-values and
    • MINP (minimum p-value).
  • fps-all: script to run pairwise search followed by fps
  • fps-sw: script to run Smith-Waterman search and prepare output for fps; requires Compugen Biocellerator or BioXL/P
  • fps-blast: script to run BLAST and prepare output for fps; requires gapped-blast 2.0 or higher
  • FPS website