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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
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