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1 gpalindrome
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2 Function
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3
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4 Searches palindrome sequences
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5
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6 Description
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7
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8 gpalindrome searches for palindrome sequences in the genome.
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9 Search parameters can be changed for more efficient searches, and g-t
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10 matching can be specified by passing the "-gtmatch" qualifier.
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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 gpalindrome
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30
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31 % gpalindrome refseqn:NC_000913
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32 Searches palindrome sequences
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33 Program compseq output file [nc_000913.gpalindrome]:
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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 [-outfile] outfile [*.gpalindrome] Program compseq output file
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44
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45 Additional (Optional) qualifiers: (none)
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46 Advanced (Unprompted) qualifiers:
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47 -shortest integer [4] Shortest palindrome to search (Any
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48 integer value)
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49 -loop integer [0] Longest stem loop to allow (Any integer
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50 value)
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51 -gtmatch boolean [0] If 1, allows g-t match
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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 -odirectory2 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 gpalindrome 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 gpalindrome is to a plain text file.
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106
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107 File: nc_000913.gpalindrome
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108
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109 Sequence: NC_000913
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110 Length, start, end, sequence
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111 4,16,18,tg ca
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112 4,27,29,at at
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113 4,44,46,tt aa
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114 4,67,69,ag ct
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115 4,97,99,aa tt
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116 4,99,101,tt aa
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117 10,100,108,taaaa tttta
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118 4,132,134,tt aa
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119
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120 [Part of this file has been deleted for brevity]
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121
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122 4,4639484,4639486,tg ca
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123 6,4639487,4639491,aag ctt
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124 4,4639495,4639497,cg cg
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125 4,4639506,4639508,ca tg
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126 6,4639552,4639556,gtc gac
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127 4,4639607,4639609,tg ca
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128 4,4639619,4639621,tg ca
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129 4,4639621,4639623,ca tg
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130 4,4639625,4639627,at at
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131 4,4639637,4639639,at at
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132
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133
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134 Data files
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135
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136 None.
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137
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138 Notes
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139
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140 None.
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141
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142 References
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143
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144 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
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145 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
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146 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
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147
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148 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
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149 large-scale analysis of high-throughput omics data, J. Pest Sci.,
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150 31, 7.
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151
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152 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
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153 Analysis Environment with REST and SOAP Web Service Interfaces,
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154 Nucleic Acids Res., 38, W700-W705.
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155
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156 Warnings
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157
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158 None.
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159
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160 Diagnostic Error Messages
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161
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162 None.
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163
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164 Exit status
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165
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166 It always exits with a status of 0.
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167
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168 Known bugs
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169
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170 None.
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171
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172 See also
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173
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174 gconsensus_z Calculate consensus in given array of sequences
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175 gdist_in_cc Calculates the distance between two loci in circular chromosomes
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176 gseqinfo Prints out basic nucleotide sequence statistics
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177
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178 Author(s)
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179
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180 Hidetoshi Itaya (celery@g-language.org)
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181 Institute for Advanced Biosciences, Keio University
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182 252-0882 Japan
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183
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184 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
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185 Institute for Advanced Biosciences, Keio University
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186 252-0882 Japan
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187
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188 History
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189
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190 2012 - Written by Hidetoshi Itaya
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191 2013 - Fixed by Hidetoshi Itaya
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192
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193 Target users
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194
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195 This program is intended to be used by everyone and everything, from
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196 naive users to embedded scripts.
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197
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198 Comments
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199
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200 None.
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201
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