Sam,

I read your X-Landscsape article in Bioinformatics and have
tried out the program. It takes awhile to get used to it,
but now that I have played with it a bit, I am beginning
to see its usefulness. I do have some comments:

1) File formats. It would be nice if the program could
read a more common format, such as fasta. Barring that,
It would also be helpful if multiple sequences could
be read from a single file. That would make it easier
to automate launching xland from GDE.

2) Neither the paper nor readme.txt makes it clear
how a database is to be made. I have experimented
with reading a file containing a bunch of 
sequences in fasta format, and I guess what 
xland is doing is to just read in all legal 
nucleotide characters, including the sequence
names, as part of a very long sequence. Probably
that doesn't make a significant difference.

If my interpretation is correct, then the way
to make a database is to create a file containing
only the raw sequences, with no names. This 
will be correct, other than for a few words created
by the junctions between sequences. 

3) It would be helpful it xland could write out a
character landscape to an ASCII file. Such files
would be smaller than PostScript, and could
be printed on any printer.

4) Unless there's a reason not to do this, it
might be best to get rid of the Index button
and just have xland automatically index each
sequence as it is read in.

5) When I try to print  Display's Write menu
using 'Send to printer', it appears that the
filter commands are executed properly, but
I get an error message

Sent to printer  (Default) xwd-pnm-ps xwd -id 0x6c000dd | /usr/local/pdsoft/bin/xwdtopnm | /usr/local/pdsoft/bin/pnmtops |lpr -P bldgagric.plant_hp3si
xwdtopnm: writing PPM file
pnmtops: maxval of 1023 is too large for PostScript
lpr: stdin: empty input file

This may be an artifact that has something to do
with pnmtops on our system.

6) It might help to add to your instructions for
installation that '/usr/openwin/lib' needs to be
in the LD_LIBRARY_PATH environment variable.
Normally that should be true, but I had been
playing around with LD_LIBRARY_PATH and somehow
that got omitted.

I guess that's all my comments for now. I'm 
hoping that landscapes may provide some insight
into plant promoters that we are studying that are
activated pathogens. Thanks for making the program
available.

===============================================================================
Brian Fristensky                | 
Department of Plant Science     |  "... the lingering after-winter, 
University of Manitoba          |   the gray season, March and April,
Winnipeg, MB R3T 2N2  CANADA    |  the months God created to show 
frist@cc.umanitoba.ca           |  people who don't drink what a
Office phone:   204-474-6085    |  hangover is like."
FAX:            204-474-7528    |            - Garrison Keillor
http://home.cc.umanitoba.ca/~frist/          WOBEGON BOY
===============================================================================