What Genotator needs in order to run on your site
Genotator is a workbench for sequence annotation.
It is available free of charge to non-profit institutions. Genotator is
written in perl using the bioTkperl widgets developed by Gregg Helt. It
can run on any Unix-like operating system that has perl and Tkperl; it
has been tested on Suns (running Solaris 1 or 2), SGIs, DEC Alphas, and
machines running Linux. The browser is straightforward to install
offsite; the back end is more complex because it expects to find
various sequence analysis tools (BLAST, gene finders, etc.), some of
which are not available offsite. The back end is set up so that it can
run with any subset of the analysis tools it is expecting, but if you're
missing most of them, the results won't be very interesting.
Genotator browser requires:
Optional accessories for the browser:
- Blixem (for displaying GenPept blast hits):
Get from
ftp://ftp.cgr.ki.se/pub/prog/MSPcrunch+Blixem/ (A version for Solaris is included with the Genotator distribution.)
- Primer3:
Get from http://www-genome.wi.mit.edu/genome_software/other/primer3.html. (A version for SunOS/Solaris is included with the Genotator distribution.)
- process-hits and process-blast.pl (by Nomi)
Included in Genotator distribution.
- xwd and xwd2ps:
These programs, which should be included with the X11 distribution, are needed if you'd like to print Genotator displays directly from Genotator. I include a version for SunOS/Solaris with the Genotator distribution, but if you're running some other operating system (e.g. Irix or Ultrix) you can try downloading the xwd2ps source from ftp://export.lcs.mit.edu/R5contrib/xwd2ps.tar.Z
Note: I wasn't able to compile it, but Sheng Wang contributed this fix:
"It turns out that the
/usr/X11R6/lib directory isn't part of the default ld(1) search path, so I needed to
have the flag "-L/usr/X11R6/lib" somewhere before "-lX11" in the offending command."
- Netscape Navigator (or Communicator):
This is needed if you want to be able to display GenBank records from Genotator.
Genotator uses wwwgrab.pm to fetch GenBank records via a Web socket.
One user reported a problem with including wwwgrab.pm. If this happens to you, you may have to comment out the line in the browser that says
use wwwgrab;
Genotator (back end) uses:
(Note: all of the sequence analysis programs are optional; if you're missing one of them,
Genotator will leave that row blank, or, in some cases, leave out the
row. But it's not really worth your while to run Genotator if you can't
get most of these sequence analysis programs set up at your site.)
Gene finders:
- GRAIL:
=ftp://ftp.lsd.ornl.gov/grailclnt
NEW as of May 2002: grailclnt is available as a perl script,
grailclnt.pl; it is included with the Genotator back end distribution.
- Genefinder:
email Colin Wilson (colin@genes.biotech.washington.edu)
or try downloading from ftp://ftp.genome.washington.edu/src/ (you need the genefinder, libutil, and tables tar files).
[I had trouble getting these to compile. Joachim Reichelt told me that he got them to compile
by changing the function name ReStrict (in makegene.c) to something else, because "restrict" is a reserved word
in gcc.]
- GENSCAN:
Contact Chris Burge (cburge@mit.edu) for executable.
- Genie:
David Kulp and Martin Reese.
- xpound:
email alun@myriad.com
Other programs:
My scripts
All of these are included in the Genotator distribution:
- find-start-and-stop
- process-hits
- parse-gf
- parse-gf-for-orfs
- parse-grail
- parse-genscan
About Genotator
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Last modified: Fri Jan 21 12:12:58 PST 2005