1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
|
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%% %%%%%
%%%%% Default parameter settings for the LaTeX ``TeXshade'' package %%%%%
%%%%% %%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%% %%%%%
%%%%% This example file contains all standard settings of the TeXshade %%%%%
%%%%% package. It can be used as a template for the creation of perso- %%%%%
%%%%% nal parameter files. All TeXshade user commands are allowed and %%%%%
%%%%% functional when specified here. %%%%%
%%%%% %%%%%
%%%%% To activate these settings for your alignment load this file by %%%%%
%%%%% naming it as optional parameter at the beginning of the texshade %%%%%
%%%%% environment, e.g. %%%%%
%%%%% %%%%%
%%%%% \begin{texshade}[myparameterfile]{alignmentfile} %%%%%
%%%%% . %%%%%
%%%%% . %%%%%
%%%%% \end{texshade} %%%%%
%%%%% %%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\shadingmode{identical} % Shade identical residues only
\shadingcolors{blues} % Select the blue color scheme for shading
\constoallseqs % Calculate consensus considering all seqs
\threshold{50} % Consensus threshold percentage is 50
\residuesperline{999} % As many residues as possible per line
\numberingwidth{9999} % Assign space for 4 digit numbering
\charstretch{1.15} % Stretch character width 1.15fold
\linestretch{1} % Do not stretch lines
\gapchar{.} % . is printed in sequence gaps
\gaprule{0.3pt} % If a rule is printed in gaps use 0.3 pt
\gapcolors{Black}{White} % Gap symbols appear `Black on White'
\numberingcolor{Black} % Numbering color is `Black'
\shownumbering{left} % Show sequence numbering on the left
\namescolor{Black} % Names' color is `Black'
\shownames{right} % Show sequence names on the right
\consensuscolors{Black}{White} % All consensus symbols/letters
{Black}{White} % appear `Black on White'
{Black}{White} %
\showconsensus{bottom} % Show consensus line at bottom with
\defconsensus{{}}{*}{!} % Blank =no match; * =match; ! =all match
\rulercolor{Black} % Ruler's color is `Black'
\hideruler % Do not show the ruler
\showleadinggaps % Show gap symbols before sequence start
\rulersteps{10} % Ruler ticks every 10 residues
\legendcolor{Black} % Legend text color is `Black'
\hidelegend % Do not show the legend
\alignment{center} % Center alignment on page
\medsepline % Medium height if separation line is on
\medblockskip % Medium skip between sequence blocks
\flexblockspace % Use optimized space between blocks
\featurerule{0.5ex} % Set feature rule thickness to 1/5 ex
\bargraphstretch{1} % Do not stretch bars in feature graphs
\colorscalestretch{1} % Do not stretch color scales in features
\backtranstext{horizontal} % Horizontal triplets in feature texts
\backtranslabel{alternating} % Alternating triplets in feature styles
\setfamily{residues}{tt} % Use typewriter family for residues
\setseries{residues}{md} % Use normal series for residues
\setshape {residues}{up} % Use upright shape for residues
\setsize {residues}{normalsize} % Use normal size for residues
\setfamily{numbering}{tt} % Use typewriter family for numbering
\setseries{numbering}{md} % Use normal series for numbering
\setshape {numbering}{up} % Use upright shape for numbering
\setsize {numbering}{normalsize} % Use normal size for numbering
\setfamily{names}{tt} % Use typewriter family for names
\setseries{names}{md} % Use normal series for names
\setshape {names}{up} % Use upright shape for names
\setsize {names}{normalsize} % Use normal size for names
\setfamily{features}{rm} % Use roman family for feature texts
\setseries{features}{md} % Use normal series for feature texts
\setshape {features}{it} % Use italics shape for feature texts
\setsize {features}{normalsize} % Use normal size for feature texts
\setfamily{legend}{tt} % Use typewriter family for legend texts
\setseries{legend}{md} % Use normal series for legend texts
\setshape {legend}{up} % Use upright shape for legend texts
\setsize {legend}{normalsize} % Use normal size for legend texts
\tintdefault{medium} % Use medium tint intensity
\emphdefault{it} % Use italics to emphasize regions
\showonPHDsec{alpha,beta} % Show helices and strands (PHD input)
\showonPHDtopo{internal,external,TM}% Show int., ext. and TM's (PHD input)
\showonHMMTOP{TM} % Show TM's (not int/ext on HMMTOP input)
\showonSTRIDE{alpha,3-10,pi,beta} % Show helices and strands (STRIDE input)
\showonDSSP{alpha,3-10,pi,beta} % Show helices and strands (DSSP input)
\secondcolumnDSSP % Use numbering from 2. column in DSSP
\appearance{PHDtopo}{internal} % \
{bottom}{'-'} % \
{int.\ \Alphacount} % |
\appearance{PHDtopo}{external} % |
{top}{,-,} % |
{ext.\ \Alphacount} % |
\appearance{PHDtopo}{TM}{top} % |
{box[LightGray]:TM\numcount}{} % |
\appearance{HMMTOP}{internal} % |
{bottom}{---} % |
{int.\ \Alphacount} % |
\appearance{HMMTOP}{external} % |
{top}{---} % |
{ext.\ \Alphacount} % |
\appearance{HMMTOP}{TM}{top} % |
{helix}{TM\numcount} % |
\appearance{PHDsec}{alpha}{top} % |
{box:$\alpha$\numcount}{} % |
\appearance{PHDsec}{beta}{top} % |
{-->}{$\beta$\numcount} % |
\appearance{STRIDE}{alpha}{top} % |
{box:$\alpha$\numcount}{} % | Definitions for the appearance of
\appearance{STRIDE}{3-10}{top} % \
{fill:$\circ$}{3$_{10}$} % > secondary structures included from|
\appearance{STRIDE}{pi} % /
{top}{---}{$\pi$} % | PHD-, STRIDE-, or DSSP-files.
\appearance{STRIDE}{beta}{top} % |
{-->}{$\beta$\numcount} % |
\appearance{STRIDE}{bridge} % |
{top}{fill:$\uparrow$}{} % |
\appearance{STRIDE}{turn} % |
{top}{,-,}{turn} % |
\appearance{DSSP}{alpha}{top} % |
{box:$\alpha$\numcount}{} % |
\appearance{DSSP}{3-10}{top} % |
{fill:$\circ$}{3$_{10}$} % |
\appearance{DSSP}{pi} % |
{top}{---}{$\pi$} % |
\appearance{DSSP}{beta}{top} % |
{-->}{$\beta$\numcount} % |
\appearance{DSSP}{bridge} % |
{top}{fill:$\uparrow$}{} % |
\appearance{DSSP}{turn} % |
{top}{,-,}{turn} % |
\appearance{DSSP}{bend}{top} % /
{fill:$\diamond$}{} % /
\pepgroups{FYW,ILVM,RK,DE,GA,ST,NQ} % Amino acid grouping due to similarity
\pepsims{F}{YW} % Y and W are similar to F
\pepsims{Y}{WF} % W and F are similar to Y
\pepsims{W}{YF} % Y and F are similar to W
\pepsims{I}{LVM} % L, V and M are similar to I
\pepsims{L}{VMI} % V, M and I are similar to L
\pepsims{V}{MIL} % M, I and L are similar to V
\pepsims{R}{KH} % K and H are similar to R
\pepsims{K}{HR} % H and R are similar to K
\pepsims{H}{RK} % R and K are similar to H
\pepsims{A}{GS} % G and S are similar to A
\pepsims{G}{A} % A (but not S) is similar to G
\pepsims{S}{TA} % T and A are similar to S
\pepsims{T}{S} % S (but not A) is similar to T
\pepsims{D}{EN} % E and N (but not Q) are similar to D
\pepsims{E}{DQ} % D and Q (but not N) are similar to E
\pepsims{N}{QD} % Q and D (but not E) are similar to N
\pepsims{Q}{NE} % N and E (but not D) are similar to Q
\DNAgroups{GAR,CTY} % Nucleotide grouping due to similarity
\DNAsims{A}{GR} % G and R are similar to A
\DNAsims{G}{AR} % A and R are similar to G
\DNAsims{R}{AG} % A and G are similar to R
\DNAsims{C}{TY} % T and Y are similar to C
\DNAsims{T}{CY} % C and Y are similar to T
\DNAsims{Y}{CT} % C and T are similar to Y
|
