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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 13, 1997
XYLEM 1.8.2 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.
Current XYLEM Version: 1.8.2 March 13, 1997
1. FETCH and FINDKEY have been updated to work with HTG and GSS
divisions of GenBank.
2. Procedure RGB has been modified to be more forgiving of
errors in GenBank entries that might otherwise cause
GETOB to loop infinitely. Now, if the first column of
a line doesn't match a legal field identifier (eg. L for
LOCUS) it will simply keep reading until if finds one.
This fix is primarily aimed at GDE, which really messes up
a number of fields, but may help with GenBank entries that
have been filtered through other programs.
3. MAXSEQ for REFORM has been increased from 50 to 200, allowing
200 sequences with a maximum length of 2000, to be printed.
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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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Brian Fristensky |
Department of Plant Science | There are more elk than people in Wallowa
University of Manitoba | County. The people like it that way.
Winnipeg, MB R3T 2N2 CANADA | So, most likely do the elk.
frist at cc.umanitoba.ca |
Office phone: 204-474-6085 | Jonathan Nicholas, 1989
FAX: 204-261-5732 | Plaque in Oregon Convention Center
http://home.cc.umanitoba.ca/~frist/
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