annotate GEMBASSY-1.0.3/doc/text/gfindoriter.txt @ 1:84a17b3fad1f draft

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1 gfindoriter
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2 Function
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3
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4 Predict the replication origin and terminus in bacterial genomes
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5
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6 Description
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7
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8 gfindoriter predicts the replicational origin and terminus in circular
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9 bacterial genomes, by taking the vertices of cumulative skew graphs (GC,
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10 d keto, or purine). See Frank and Lobry (2000) for the basic idea behind
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11 this algorithm (but also note that this algorithm is different from that
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12 of Oriloc, which uses GC3 of genes).
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13 Terminus of replication can be more accurate by using noise-reduction
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14 filtering using Fourier spectrum of the GC skew. This low-pass filtering
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15 can be applied using -filter option. See Arakawa et al. (2007) for details.
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16
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17 G-language SOAP service is provided by the
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18 Institute for Advanced Biosciences, Keio University.
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19 The original web service is located at the following URL:
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20
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21 http://www.g-language.org/wiki/soap
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22
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23 WSDL(RPC/Encoded) file is located at:
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24
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25 http://soap.g-language.org/g-language.wsdl
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26
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27 Documentation on G-language Genome Analysis Environment methods are
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28 provided at the Document Center
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29
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30 http://ws.g-language.org/gdoc/
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31
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32 Usage
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33
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34 Here is a sample session with gfindoriter
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35
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36 % gfindoriter refseqn:NC_000913
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37 Predict the replication origin and terminus in bacterial genomes
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38 Output file [nc_000913.gfindoriter]:
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39
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40 Go to the input files for this example
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41 Go to the output files for this example
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42
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43 Command line arguments
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44
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45 Standard (Mandatory) qualifiers:
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46 [-sequence] seqall Nucleotide sequence(s) filename and optional
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47 format, or reference (input USA)
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48 [-outfile] outfile [*.gfindoriter] Output file name
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49
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50 Additional (Optional) qualifiers: (none)
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51 Advanced (Unprompted) qualifiers:
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52 -window integer [4096] Number of windows to use for Fat
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53 Fourier Transform. Only active when -lowpass
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54 option is specified. Value must be the
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55 power of two (Any integer value)
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56 -purine boolean [N] Use purine skew for calculation
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57 -keto boolean [N] Use keto skew for calculation
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58 -lowpass integer [0] Lowpass filter strength in percent.
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59 Typically 95 or 99 works best (Any integer
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60 value)
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61 -[no]accid boolean [Y] Include to use sequence accession ID as
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62 query
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63
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64 Associated qualifiers:
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65
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66 "-sequence" associated qualifiers
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67 -sbegin1 integer Start of each sequence to be used
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68 -send1 integer End of each sequence to be used
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69 -sreverse1 boolean Reverse (if DNA)
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70 -sask1 boolean Ask for begin/end/reverse
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71 -snucleotide1 boolean Sequence is nucleotide
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72 -sprotein1 boolean Sequence is protein
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73 -slower1 boolean Make lower case
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74 -supper1 boolean Make upper case
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75 -scircular1 boolean Sequence is circular
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76 -sformat1 string Input sequence format
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77 -iquery1 string Input query fields or ID list
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78 -ioffset1 integer Input start position offset
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79 -sdbname1 string Database name
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80 -sid1 string Entryname
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81 -ufo1 string UFO features
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82 -fformat1 string Features format
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83 -fopenfile1 string Features file name
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84
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85 "-outfile" associated qualifiers
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86 -odirectory2 string Output directory
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87
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88 General qualifiers:
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89 -auto boolean Turn off prompts
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90 -stdout boolean Write first file to standard output
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91 -filter boolean Read first file from standard input, write
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92 first file to standard output
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93 -options boolean Prompt for standard and additional values
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94 -debug boolean Write debug output to program.dbg
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95 -verbose boolean Report some/full command line options
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96 -help boolean Report command line options and exit. More
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97 information on associated and general
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98 qualifiers can be found with -help -verbose
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99 -warning boolean Report warnings
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100 -error boolean Report errors
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101 -fatal boolean Report fatal errors
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102 -die boolean Report dying program messages
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103 -version boolean Report version number and exit
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104
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105 Input file format
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106
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107 The database definitions for following commands are available at
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108 http://soap.g-language.org/kbws/embossrc
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109
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110 gfindoriter reads one or more nucleotide sequences.
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111
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112 Output file format
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113
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114 The output from gfindoriter is to a plain text file.
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115
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116 File: nc_000913.gfindoriter
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117
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118 Sequence: NC_000913 Origin: 3922946 Terminus: 1550274
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119
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120
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121 Data files
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122
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123 None.
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124
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125 Notes
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126
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127 None.
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128
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129 References
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130
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131 Frank AC, Lobry JR (2000) Oriloc: prediction of replication boundaries in
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132 unannotated bacterial chromosomes, Bioinformatics, 16:566-567.
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133
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134 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
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135 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
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136 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
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137
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138 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
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139 large-scale analysis of high-throughput omics data, J. Pest Sci.,
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140 31, 7.
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141
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142 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
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143 Analysis Environment with REST and SOAP Web Service Interfaces,
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144 Nucleic Acids Res., 38, W700-W705.
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145
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146 Warnings
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147
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148 None.
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149
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150 Diagnostic Error Messages
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151
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152 None.
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153
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154 Exit status
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155
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156 It always exits with a status of 0.
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157
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158 Known bugs
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159
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160 None.
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161
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162 See also
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163
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164 greporiter Gets the positions of replication origin and terminus
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165
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166 Author(s)
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167
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168 Hidetoshi Itaya (celery@g-language.org)
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169 Institute for Advanced Biosciences, Keio University
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170 252-0882 Japan
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171
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172 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
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173 Institute for Advanced Biosciences, Keio University
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174 252-0882 Japan
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175
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176 History
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177
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178 2012 - Written by Hidetoshi Itaya
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179 2013 - Fixed by Hidetoshi Itaya
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180
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181 Target users
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182
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183 This program is intended to be used by everyone and everything, from
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184 naive users to embedded scripts.
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185
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186 Comments
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187
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188 None.
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189