XYLEM Database Tools - Version 1.8.1

Brian Fristensky frist at cc.umanitoba.ca
Mon Mar 4 18:48:34 EST 1996


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    Fristensky, B. (1993) Feature expressions: creating and manipulating
    sequence datasets. Nucl. Acids Res. 21:5997-6003.
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March 4, 1996

XYLEM 1.8.1 is now available by anonymous FTP in directory 'psgendb' at 
ftp.cc.umanitoba.ca or by WWW from http://home.cc.umanitoba.ca/~psgendb/.

XYLEM is a package of tools designed to exploit the Unix
environment to enable the user to identify, extract and
manipulate data from major databases such as GenBank and
PIR. Fundamental to the power of these programs is the ability to
perform operations on groups of sequences, represented by names
or accession numbers which function as virtual database subsets.
The most powerful program is FEATURES, which uses the GETOB parser 
to evaluate GenBank/EMBL/DDBJ Features Table expressions, thereby
extract features (eg. mRNA, sig_peptide, intron) from lists of
entries. Additional programs perform operations such as translation
or randomization of datasets, and formatting of multiply-aligned sequences
for publication. XYLEM is compatible with the Fristensky Sequence
Analysis Package, and the Pearson FASTA programs, and can be used
from within the Genetic Data Environment (GDE) of Steven Smith.

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Current XYLEM Version: 1.8.1           March 1, 1996

1. Remote execution of FETCH and FINDKEY can now be done on
multiple servers, chosen in rotation, from job to job.
2. FINDKEY and FETCH now allow an arbitrary number of files in the
GenBank EST division (gbest1, gbest2, gbest3...)

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Version: 1.8           February 13, 1996


1. FEATURES has been upgraded to work with 8-character accession numbers.

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Version: 1.7           January 27, 1996

1. The Expressed Sequence Tag division of GenBank is now distributed
in two files, gbest1.seq and gbest2.seq. fetch.csh, findkey.csh and gbupdate 
have been modified to be able to work with the EST division so that
this change is transparent to the user.

2. FINDKEY and FETCH now call cpu-intensive programs (eg. SPLITDB,
GETLOC) using 'nice', which decreases the impact of these programs
on system performance.

3. GETOB now recognizes GenBank NID lines.

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Version: 1.6           October 3, 1995

1. As of February 1996, GenBank and EMBL will begin assigning 8 character
accession numbers to new entries. Old entries will retain their 6 
character accession numbers. SPLITDB, FINDKEY, and UDS have
been updated to comply with this change. All other programs should be
unaffected.

2. uds.csh has been substantially revised. Previous versions would sometimes
lose entries.

3. The file xylem/GDE/expfile.template has been updated with more
accurate instructions for retrieval of sequences by expressions
using the FEATURES program.

4. Documentation for FETCH, FINDKEY, GETOB, and SPLITDB has been 
updated.

5. Routines that automatically download GenBank and PIR by FTP
(gbupdate and pirupdate) have been made a bit more reliable.

6. GETLOC has been updated to be able to use unsorted namefiles.

7. SPLITDB -c will compress leading blanks when creating .ano files.
This saves ~ 9% of the space normally taken up by an annotation file.
GETLOC and GETOB automatically uncompress these blanks, if they
have been compressed. However, the .fnd file from FINDKEY will
retrieve lines without uncompressing the blanks. The output is
a little less elegant, but accomplishes the same thing.

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Version: 1.5           October 29, 1994

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

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     |  The optimist proclaims that we live in
University of Manitoba          |  the best of all possible worlds. The
Winnipeg, MB R3T 2N2  CANADA    |  pessimist fears that this is true.
frist at cc.umanitoba.ca           |
Office phone:   204-474-6085    |  James Branch Cabell (1879-1958)
FAX:            204-261-5732    |
http://home.cc.umanitoba.ca/~frist/
===============================================================================


 








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