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XYLEM 1.8.2
Introduction
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 randomisation 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.
New in this version
FETCH and FINDKEY have been updated to work with HTG andGSS divisions of GenBank.
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.
MAXSEQ for REFORM has been increased from 50 to 200, allowing 200 sequences with a maximum length of 2000, to be printed.
Availability
XYLEM 1.8.2 is freely available by anonymous FTP in from the University of Manitoba.
Information provided by: Brian Fristensky
Resources and further information
University of Manitoba
http://www.umanitoba.ca/
Department of Plant Science
http://www.umanitoba.ca/faculties/agricultural_and_food_sci ences/
plant_science/Plant_Science.html
XYLEM homepage
http://home.cc.umanitoba.ca/~psgendb/XYLEM.h tml
Download XYLEM
ftp://ftp.cc.umanitoba.ca/psgendb/
Literature:
Fristensky, B. (1993) Feature expressions: creating and manipulating sequence datasets. Nucl. Acids Res. 21:5997-6003.
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