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The RBS pattern file is simply a file containing a table of frequencies with which nucleotides occur at a given position within the ribosome binding site. This information is used when evaluating the the starts of open reading frames.

The values for the RBS pattern file (see below) are determined by aligning all known RBS sites and transcribing the frequency that the specified nucleotide appears at the given position in the RBS.

... a sample RBS pattern file:

# This is a sample RBS site description file for use with GeneMark
#
# The format of this file is quite simple. Anything after the '#' symbol on
# any line is ignored. Any character after the nucleotide tag other than the
# numbers 0-9 and the decimal point are ignored (you can use a comma in place
# of the decimal point). All other characters are interpretted as whitespace.
# All of the number must be in the range from 0 to 1 (probability values).
#
#
# For example:
# Position
# 1 2 3 4 5 6  
# ----- ----- ----- ----- ----- -----  
T 0.10 0.21 0.12 0.04 0.09 0.13 # T values
C 0.34 0.14 0.04 0.05 0.06 0.05 # C values
A 0.39 0.58 0.11 0.08 0.70 0.21 # A values
G 0.19 0.09 0.75 0.84 0.16 0.61 # G values
#
# Simple enough, n'est-ce pas?
#
# One more thing: This file should be somewhere in the search path for the
# matrix file (the environment variable MATPATH) or the current directory.


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