XYLEM Database Package, Release 1.5

Brian Fristensky frist at cc.umanitoba.ca
Sat Oct 29 18:59:24 EST 1994


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Version 1.5 of the XYLEM Database Package, as described in

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

is now available by anonymous FTP to directory 'psgendb' at
ftp.cc.umanitoba.ca. 
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The XYLEM programs provide powerful and easy to use interfaces for
finding and retrieving entries from GenBank, PIR, and other databases.
Unique to XYLEM is the FEATURES program, which can extract subsequences
from GenBank entries based on annotation in the Features Table.

   SUMMARY: WHAT'S NEW IN XYLEM 1.5:
        - now works with the new GenBank Sequence Tagged Sites division
        - translation from Pascal to C speeds up execution,
          expands portability 
        - new program: PROT2NUC (reverse translation) 
        - can handle largest sequences in GenBank

------------------------------------------------------------------------       
Specific changes in version 1.5 are as follows: 

1. All XYLEM programs are now available as both the original Pascal
source code as well as C code generated by p2c. The C code has been
tested with the following compilers:

compiler   platform
-------------------
  cc       Sun
  cc       HP/UX
  gcc      Sun
  gcc      AIX

It is worth noting that code compiled under Sun cc runs over 50% faster
than the original Pascal code compiled with Sun Pascal 2.0. For that
reason, Sparc binaries distributed by FTP  are now generated from C-code,
rather than Pascal.

2. FETCH and FINDKEY can now access the STS division of GenBank, which
was added with GenBank Release 85.0 The .GDEmenus entry for FINDKEY has
been changed accordingly.

3. A bug has been fixed in FETCH that in some case would cause FETCH
to fail when retrieving entries from VecBase.

4. The following modifications have been made to GETOB:
     13 Oct 94 Initialize NUMN. Failure to initialize causes n's to be written
               to expression file for non-translated features.               
     13 Oct 94 MAXSEQ increased to 750,000
     11 Sep 94 Added ability to handle single base_position as a location. 
      9 Sep 94 If codon_start=2,3, write n's to expression file, as is
               already done for outfile.
     13 Apr 94 Literature citation in .msg file
      2 Jan 94 add NCBI_GI field
     25 Oct 93 Fixed bug in COMPLEMENT. Only complemented 3' most location
               in an expression of the form complement(join(L1,L2..Ln))

5. PROT2NUC - new program, performs reverse translation of protein to DNA.

===============================================================================
Brian Fristensky                | 
Department of Plant Science     |  Life doesn't imitate art,
University of Manitoba          |  it imitates bad television. 
Winnipeg, MB R3T 2N2  CANADA    |  
frist at cc.umanitoba.ca           |  
Office phone:   204-474-6085    |  Woody Allen, HUSBANDS AND WIVES  
FAX:            204-261-5732    |  
===============================================================================




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