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2 /* GEMBASSY ver 1.0.3 *********************************************************
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3
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4 All rights reserved. Copyright (C) 2012-2013 by ITAYA Hidetoshi.
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5
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6 This EMBASSY package is free software. You can redistribute it and/or modify
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7 it under the terms of the GNU General Public License as published by the
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8 Free Software Foundation, either version 2 of the License, or any later
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9 version.
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10
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11 See also GNU General Public License Version 2, included in this
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12 package as COPYING.
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13
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14 *****************************************************************************/
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15
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16
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17
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18 /* About *********************************************************************
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19
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20 This is an EMBASSY package for the utilization of G-language SOAP service.
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21
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22 All of the tools included in this package are wrapper programs to
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23 utilize G-language SOAP service, which are web APIs to access the methods
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24 of G-language Genome Analysis Environment (G-language GAE); a powerful
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25 workbench for genome analysis.
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26
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27 Detailed documentation on G-language GAE methods are availabe at:
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28 http://www.g-language.org/wiki/soap
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29
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30 The EMBOSS Explorer interface is available at:
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31 http://soap.g-language.org/gembassy/emboss_explorer
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32
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33 *****************************************************************************/
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34
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35
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36
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37 /* Installation **************************************************************
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38
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39 REQUIREMENTS
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40 EMBOSS (> 6.6.0) - This EMBASSY package requires EMBOSS version 6.6.0 or
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41 above.
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42 libcurl-devel (> 7.29.0) - Required for file POST
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43
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44 A UNIX-like operating system
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45
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46 INSTALLATION
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47 Is EMBOSS already installed in your system?
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48 Yes: Go to "EMBOSS is already installed" section.
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49 No: Go to "Install from EMBOSS" section.
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50
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51 Install from EMBOSS:
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52 Root users
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53 In the following examples we assume the downloaded EMBOSS archive filename
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54 is emboss-latest.tar.gz
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55
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56 1. Download and compile EMBOSS source code
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57 % wget ftp://emboss.open-bio.org/pub/EMBOSS/emboss-latest.tar.gz
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58 (or "curl -O ftp://emboss.open-bio.org/pub/EMBOSS/emboss-latest.tar.gz")
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59 % tar zxf emboss-latest.tar.gz
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60 % cd EMBOSS-6.6.0
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61 % ./configure
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62 % make
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63 % sudo make install
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64
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65 2. Make "embassy" directory in the EMBOSS-6.6.0/ directory if it does not
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66 exist and go into the directory.
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67 % mkdir embassy
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68 % cd embassy
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69
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70 3. Download and compile the GEMBASSY source code
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71 % wget http://soap.g-language.org/gembassy/source/GEMBASSSY-1.0.3.tar.gz
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72 (or "curl -O http://soap.g-language.org/gembassy/source/GEMBASSY-1.0.3.tar.gz")
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73 % tar zxvf GEMBASSY-1.0.3.tar.gz
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74 % cd GEMBASSY-1.0.3
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75 ( EMBOSS-6.6.0/embassy/GEMBASSY-1.0.3 )
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76 % ./configure
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77 % make
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78 % sudo make install
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79
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80 Non-root users
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81 When running the './configure' command do the following instead:
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82 % ./configure --prefix=/PATH/TO/DIR/ (ex. --prefix=$HOME/opt)
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83
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84 EMBOSS is already installed:
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85 When EMBOSS is already installed, GEMBASSY must be installed to the exact
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86 same directory as the existing EMBOSS.
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87
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88 If non-root users wish to install GEMBASSY separately, first install the
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89 EMBOSS package on top of the home directory.
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90
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91 The following commands assume you have EMBOSS installed in the
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92 /PATH/TO/EMBOSS/ directory.
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93 % wget http://soap.g-language.org/gembassy/source/GEMBASSY-1.0.3.tar.gz
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94 (or "curl -O http://soap.g-language.org/gembassy/source/GEMBASSY-1.0.3.tar.gz")
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95 % tar zxf GEMBASSY-1.0.3.tar.gz
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96 % cd GEMBASSY-1.0.3
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97 % ./configure --prefix=/PATH/TO/EMBOSS/ (ex. --prefix=/usr/local)
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98 % make
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99 % make install
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100
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101
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102 Installing custom EMBOSS configuration files
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103 We highly recommend users to install the custom EMBOSS configuration files
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104 from the KBWS package. The configuration file provides database definition
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105 for various databases, allowing versatile access to various sequence
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106 entries.
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107
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108 % wget http://soap.g-language.org/kbws/embossrc
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109 (or "curl -O http://soap.g-language.org/kbws/embossrc")
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110 % mv embossrc ~/.embossrc
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111
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112 Then rewrite the "emboss_acdroot" and "emboss_data" value in ~/.embossrc
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113 file to the corresponding directories.
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114 (ex. emboss_acdroot = ~/opt/share/EMBOSS/acd)
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115 (ex. emboss_data = ~/opt/share/EMBOSS/data)
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116
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117 Update of EMBOSS
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118 When users are upgrading EMBOSS, please be sure to uninstall old versions
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119 of EMBOSS and GEMBASSY. If you override them, some older versions of files
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120 may cause errors.
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121
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122 NOTE - automake problem
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123 If the source code is cloned from the GitHub Repository, there are
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124 known problems with automake version mismatches which stop the compilation
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125 of the source. Follow the steps below in (NOTE - libtool problem) to
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126 solve this problem.
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127
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128 NOTE - libtool problem
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129 On some systems there may be compatibility problems with different
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130 automake, autoconf or libtool versions. If a libtool problem
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131 arises you can try deleting the following files if they exist:
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132
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133 config.cache
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134 ltmain.sh
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135 ltconfig
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136 libtool
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137
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138 and then type
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139 % aclocal -I m4
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140 % autoconf
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141 % automake -a
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142
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143 and then retry make.
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144
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145 If you have 'autoreconf' in your system
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146 % autoreconf -fi
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147
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148 will do the trick.
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149
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150 *****************************************************************************/
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151
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152
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153
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154 /* QuickStart ****************************************************************
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155
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156 DATABASE DEFINITION
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157 The database definitions for following commands are available at
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158 http://soap.g-language.org/kbws/embossrc
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159 Input files used in the examples are provided in the data/ directory.
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160
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161 INSTALLATION:
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162 % wget http://soap.g-language.org/kbws/embossrc
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163 (or "curl -O http://soap.g-language.org/kbws/embossrc")
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164 % mv embossrc ~/.embossrc
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165
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166 Then rewrite the "emboss_acdroot" and "emboss_data" value in ~/.embossrc
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167 file to the corresponding directories.
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168 (ex. emboss_acdroot = ~/share/EMBOSS/acd)
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169 (ex. emboss_data = ~/share/EMBOSS/data)
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170
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171 INFORMATION OF GEMBASSY TOOLS
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172 List of all tools
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173 For a list of all tools included in GEMBASSY use
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174 % wossname -showembassy GEMBASSY
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175
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176 Documentation
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177 Detailed documentation are available to be viewed with the "tfm"
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178 utility included in EMBOSS.
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179 Here is an example for "gaminoinfo"
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180 % tfm gaminoinfo
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181
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182 USAGE EXAMPLE
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183 The following examples show basic usages of three GEMBASSY tools and the
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184 different ways of passing input. Example 1. uses database definition, 2.
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185 uses the accid option, and 3. uses the sequence accession ID as input.
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186 1. ggcskew (GC skew)
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187 % ggcskew -plot -graph cps refseqn:NC_000913
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188 Calculates the GC skew of the input sequence
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189 Created ggcskew.ps
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190
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191 2. ggcsi (GC Skew Index)
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192 % ggcsi accid.fasta -accid stdout
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193 GC Skew Index: an index for strand-specefic mutational bias
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194 Input nucleotide sequence: refseqn:NC_000964
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195 Sequence: NC_000964 GCSI: 0.214855185905019 SA: 976.152832384745 DIST: 170.245783
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196
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197 3. greporiter (Replication Origin and Terminus)
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198 % greporiter -outfile stdout
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199 Get the positions of replication origin and terminus
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200 Input nucleotide sequence: accid.fasta
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201 Sequence: NC_000913 Origin: 3923881 Terminus: 1550412
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202
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203 *****************************************************************************/
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204
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205
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206
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207 /* Content *******************************************************************
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208
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209 gSOAP Toolkit
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210 This EMBASSY package is dependant on gSOAP Toolkit for SOAP transfer,
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211 included in the gsoap/ directory. It is used automatically during
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212 compilation.
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213
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214 *****************************************************************************/
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215
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216
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217
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218 /* Contact *******************************************************************
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219
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220 Hidetoshi Itaya (celery @ g-language.org)
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221 Institute for Advanced Biosciences, Keio University.
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222
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223 *****************************************************************************/
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