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1 gdistincc
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2 Function
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3
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4 Calculates the distance between two loci in circular chromosomes
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5
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6 Description
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7
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8 gdistincc calculates the distance between two loci in circular
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9 chromosomes. It is mostly useful to calculate the distance from the
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10 replication origin.
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11
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12 G-language SOAP service is provided by the
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13 Institute for Advanced Biosciences, Keio University.
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14 The original web service is located at the following URL:
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15
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16 http://www.g-language.org/wiki/soap
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17
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18 WSDL(RPC/Encoded) file is located at:
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19
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20 http://soap.g-language.org/g-language.wsdl
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21
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22 Documentation on G-language Genome Analysis Environment methods are
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23 provided at the Document Center
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24
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25 http://ws.g-language.org/gdoc/
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26
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27 Usage
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28
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29 Here is a sample session with gdistincc
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30
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31 % gdistincc refseqn:NC_000913 1234
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32 Calculates the distance between two loci in circular chromosomes
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33 Output file [nc_000913.gdistincc]:
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34
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35 Go to the input files for this example
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36 Go to the output files for this example
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37
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38 Command line arguments
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39
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40 Standard (Mandatory) qualifiers:
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41 [-sequence] seqall Nucleotide sequence(s) filename and optional
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42 format, or reference (input USA)
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43 [-first] integer [0] Position to find the distance (Any
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44 integer value)
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45 [-outfile] outfile [*.gdistincc] Output file name
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46
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47 Additional (Optional) qualifiers: (none)
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48 Advanced (Unprompted) qualifiers:
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49 -second integer [-1] If the second position is negative,
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50 position of replication origin is used (Any
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51 integer value)
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52 -[no]accid boolean [Y] Include to use sequence accession ID as
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53 query
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54
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55 Associated qualifiers:
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56
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57 "-sequence" associated qualifiers
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58 -sbegin1 integer Start of each sequence to be used
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59 -send1 integer End of each sequence to be used
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60 -sreverse1 boolean Reverse (if DNA)
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61 -sask1 boolean Ask for begin/end/reverse
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62 -snucleotide1 boolean Sequence is nucleotide
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63 -sprotein1 boolean Sequence is protein
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64 -slower1 boolean Make lower case
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65 -supper1 boolean Make upper case
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66 -scircular1 boolean Sequence is circular
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67 -sformat1 string Input sequence format
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68 -iquery1 string Input query fields or ID list
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69 -ioffset1 integer Input start position offset
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70 -sdbname1 string Database name
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71 -sid1 string Entryname
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72 -ufo1 string UFO features
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73 -fformat1 string Features format
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74 -fopenfile1 string Features file name
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75
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76 "-outfile" associated qualifiers
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77 -odirectory3 string Output directory
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78
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79 General qualifiers:
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80 -auto boolean Turn off prompts
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81 -stdout boolean Write first file to standard output
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82 -filter boolean Read first file from standard input, write
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83 first file to standard output
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84 -options boolean Prompt for standard and additional values
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85 -debug boolean Write debug output to program.dbg
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86 -verbose boolean Report some/full command line options
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87 -help boolean Report command line options and exit. More
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88 information on associated and general
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89 qualifiers can be found with -help -verbose
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90 -warning boolean Report warnings
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91 -error boolean Report errors
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92 -fatal boolean Report fatal errors
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93 -die boolean Report dying program messages
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94 -version boolean Report version number and exit
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95
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96 Input file format
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97
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98 The database definitions for following commands are available at
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99 http://soap.g-language.org/kbws/embossrc
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100
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101 gdistincc reads one or more nucleotide sequences.
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102
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103 Output file format
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104
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105 The output from gdistincc is to a plain text file.
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106
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107 File: nc_000913.gdistincc
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108
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109 Sequence: NC_000913 Position1: 1234 Distance 1169193600
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110
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111
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112 Data files
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113
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114 None.
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115
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116 Notes
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117
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118 None.
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119
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120 References
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121
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122 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
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123 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
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124 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
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125
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126 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
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127 large-scale analysis of high-throughput omics data, J. Pest Sci.,
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128 31, 7.
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129
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130 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
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131 Analysis Environment with REST and SOAP Web Service Interfaces,
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132 Nucleic Acids Res., 38, W700-W705.
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133
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134 Warnings
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135
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136 None.
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137
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138 Diagnostic Error Messages
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139
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140 None.
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141
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142 Exit status
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143
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144 It always exits with a status of 0.
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145
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146 Known bugs
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147
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148 None.
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149
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150 See also
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151
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152 gconsensus_z Calculate consensus in given array of sequences
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153 gpalindrome Searches palindrome sequences
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154 gseqinfo Prints out basic nucleotide sequence statistics
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155
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156 Author(s)
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157
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158 Hidetoshi Itaya (celery@g-language.org)
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159 Institute for Advanced Biosciences, Keio University
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160 252-0882 Japan
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161
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162 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
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163 Institute for Advanced Biosciences, Keio University
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164 252-0882 Japan
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165
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166 History
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167
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168 2012 - Written by Hidetoshi Itaya
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169 2013 - Fixed by Hidetoshi Itaya
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170
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171 Target users
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172
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173 This program is intended to be used by everyone and everything, from
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174 naive users to embedded scripts.
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175
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176 Comments
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177
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178 None.
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179
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