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SpecialAminoAcids.txt
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SpecialAminoAcids.txt
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# This is a config file. It is loaded by 12_ConvertTressToFigures.py.
# The values defined here are used for displaying the amino acid of
# interest in the visualized trees, and the sequences logos.
# One sequence logo displays the covers the sequences around the
# aaPos, toLowerLimit gives the number of amino acids before the
# amino acid of interest at aaPos. And toUpperLimit gives the number of amino acids
# following aaPos for the end of the sequence logo.
# seqFile is the sequence file of the reference sequence, which is the first sequence
# in that file.
# interestingAAsPos are the positions of interesting amino acid positions in
# the reference sequence for another sequence logo.
# Of course, the positions should exist in the sequence of interests. For errors
# here is the user responsible.
seqFile MustKeepSequences/NP_001014890_Rhodopsin_Bos_Taurus.fasta
aaPos 296
toLowerLimit 9
toUpperLimit 29
# Make sure those are in order, this is the order that shows up in the sequence logo
interestingAAPositions 83 110 113 134 135 136 181 185 187 296 302 303 304 305 306 313 310 311 312
# AminoAcids to highlight
aaToHighlight 292 296 302 303 304 305 306 314
#
# Highlight colors, for each amino acid a color
highlightColors DimGray DimGray DimGray DimGray DimGray DimGray DimGray DimGray