From: benson@ecology.biomath.mssm.edu
To: "@msvax.mssm.edu":@msvax.mssm.edu:compfly@bdgp.lbl.gov
Cc: benson@ecology.biomath.mssm.edu
Subject: satellite prediction experiment submission
Date: Tue, 29 Jun 1999 15:47:13 -0400 (EDT)

To the organizers of the satellite prediction experiment:

   Appended to this message is an analysis of the test sequence for
tandem repeats.  This analysis was performed by the Tandem Repeats
Finder program [G. Benson, NAR 27:573-580 (1999)].  The analysis was
done with standard parameter settings including a cutoff score of 50.
With this cutoff, a tandem repeat must extend for at least 25
nucleotides to be reported.  A lower scores could be used but would
probably increase the number of repeats that are random noise.  

  Full analysis of the test sequence required ~20 seconds.  

  The Tandem Repeats Finder program is available for public use via a
web browser at 

	    http://c3.biomath.mssm.edu/trf.html

Sequences, up to 5 Mbp can be submitted anonomously for analysis.
Output from the program is a summary table of the repeats including
information similar to that reported in the GFF file appended below.
This table is linked to a separate file which shows the alignments of
each tandem repeat to a consensus sequence.  

The summary table file for the test sequence can be viewed at

  http://c3.biomath.mssm.edu/trf/47UqmpCSrhVAA.2.7.7.80.10.50.500.1.html

This table table is linked to the alignment file.  

I will not be at the conference until Monday the 9th of August, but I
hope to speak with members of the organizing committee about the
results.  

				Best regards,

				Gary Benson

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