XYLEM package: New PIR format, other updates

frist at cc.umanitoba.ca frist at cc.umanitoba.ca
Sat Apr 16 12:40:05 EST 1994


      --------------------------------------------------------------------
      #    #   #   #  #       ######  #    #     XYLEM 
      #  #     # #   #       #       ##  ##
      ##       #    #       #####   # ## #             Database
     ##       #    #       #       #    #      
   #  #      #    #       #       #    #                         Tools
 #    #     #    ######  ######  #    # 
 ---------------------------------------------------------------------

April 16, 1994

   CONTENTS:

   1) SPECIAL ANNOUNCEMENT - New PIR format
   2) Citing XYLEM
   3) Improvements and bug fixes
   4) C source code now available


1) SPECIAL ANNOUNCEMENT - New PIR format
----------------------------------------
PIR Release 39.0 introduces extensive format changes. While most of these
do not affect XYLEM,  the keywords "ACCESSION" and "#Accession"  have
been changed to "ACCESSIONS" and "#accessions", which were not recognized
by previous versions of the program SPLITDB. SPLITDB has been updated
to read the new format.

2) Citing XYLEM
---------------
Research papers reporting results obtained with the assistance of
XYLEM programs should cite:

    Fristensky, B. (1993) Feature expressions: creating and manipulating
    sequence datasets. Nucl. Acids Res. 21:5997-6003.

There's no such thing as a free lunch. HERE is where you pay for 
the programs.

3) Improvements and bug fixes
-----------------------------

   FEATURES
      - The GDE menus now allow direct analysis of selected sequences
        (Note: Releases of this menu dating February or earlier
        would sometimes truncate sequence names, due to a bug in
        GDE. A workaround is incorporated into the current version.)
     
   FETCH
      - Several bugs have been fixed in the code allowing FETCH
        to retrieve entries on a remote host.

   FINDKEY
      - FINDKEY can now search databases on a remote host.

   Output windows - Output windows generated by GDE now more tightly
        conform to the size of the output, resulting in less screen
        clutter.

   GBUPDATE & PIRUPDATE - scripts that download GenBank and PIR have
        additional error checking, preventing accidental clobbering
        of the current copies of files during the download.   

4) C source code now available
------------------------------
The Pascal programs comprising the low-level tools of XYLEM are
now also available as C-source code, translated by David Gillespie's
p2c. The directory xylem/src.c contains C source, a Makefile,
libraries enabling easy compilation on Sun or HP/UX platforms.

XYLEM is available by anonymous FTP to directory psgendb at
ftp.cc.umanitoba.ca (130.179.16.24). 

===============================================================================
Brian Fristensky                | 
Department of Plant Science     |  A question is like a knife that slices
University of Manitoba          |  through the stage backdrop and gives us
Winnipeg, MB R3T 2N2  CANADA    |  a look at what lies hidden behind.
frist at cc.umanitoba.ca           |  
Office phone:   204-474-6085    |  Milan Kundera, THE UNBEARABLE LIGHTNESS 
FAX:            204-261-5732    |  OF BEING
===============================================================================

        







More information about the Bio-soft mailing list