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1 gldabias
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2 Function
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3
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4 Calculate strand bias of bacterial genome using linear discriminant
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5
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6 Description
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7
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8 gldabias calculates strand bias of bacterial genome using linear
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9 discriminant analysis (LDA), as proposed in Reference 1. The basic idea is
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10 to use composition data of genes to train and predict the strand of genes
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11 residing either on the leading or the lagging strand. For computational
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12 efficiency, this method trans and predicts the strands at putative
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13 replication origin as reported by the rep_ori_ter() method. This usually
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14 results in maximum predictability of LDA within bacterial genomes.
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15 Data to use for LDA can be chosen from "base", "codonbase", "codon", and
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16 "amino", with -variable option.
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17
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18 G-language SOAP service is provided by the
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19 Institute for Advanced Biosciences, Keio University.
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20 The original web service is located at the following URL:
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21
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22 http://www.g-language.org/wiki/soap
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23
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24 WSDL(RPC/Encoded) file is located at:
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25
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26 http://soap.g-language.org/g-language.wsdl
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27
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28 Documentation on G-language Genome Analysis Environment methods are
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29 provided at the Document Center
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30
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31 http://ws.g-language.org/gdoc/
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32
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33 Usage
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34
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35 Here is a sample session with gldabias
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36
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37 % gldabias refseqn:NC_000913
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38 Calculate strand bias of bacterial genome using linear discriminant
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39 analysis (LDA)
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40 Program compseq output file [nc_000913.gldabias]:
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41
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42 Go to the input files for this example
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43 Go to the output files for this example
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44
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45 Command line arguments
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46
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47 Calculate strand bias of bacterial genome using linear discriminant
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48 analysis (LDA)
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49 Version: EMBOSS:6.5.7.0 GEMBASSY:1.0.1
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50
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51 Standard (Mandatory) qualifiers:
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52 [-sequence] seqall Nucleotide sequence(s) filename and optional
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53 format, or reference (input USA)
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54 [-outfile] outfile [*.gldabias] Program compseq output file
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55
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56 Additional (Optional) qualifiers: (none)
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57 Advanced (Unprompted) qualifiers:
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58 -coefficients integer [0] Show LDA coefficients (Any integer
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59 value)
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60 -variable selection [codon] Data to use for LDA. Either 'base',
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61 'codonbase', 'codon', or 'amino'
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62 -[no]accid boolean [Y] Include to use sequence accession ID as
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63 query
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64
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65 Associated qualifiers:
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66
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67 "-sequence" associated qualifiers
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68 -sbegin1 integer Start of each sequence to be used
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69 -send1 integer End of each sequence to be used
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70 -sreverse1 boolean Reverse (if DNA)
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71 -sask1 boolean Ask for begin/end/reverse
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72 -snucleotide1 boolean Sequence is nucleotide
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73 -sprotein1 boolean Sequence is protein
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74 -slower1 boolean Make lower case
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75 -supper1 boolean Make upper case
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76 -scircular1 boolean Sequence is circular
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77 -sformat1 string Input sequence format
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78 -iquery1 string Input query fields or ID list
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79 -ioffset1 integer Input start position offset
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80 -sdbname1 string Database name
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81 -sid1 string Entryname
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82 -ufo1 string UFO features
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83 -fformat1 string Features format
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84 -fopenfile1 string Features file name
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85
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86 "-outfile" associated qualifiers
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87 -odirectory2 string Output directory
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88
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89 General qualifiers:
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90 -auto boolean Turn off prompts
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91 -stdout boolean Write first file to standard output
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92 -filter boolean Read first file from standard input, write
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93 first file to standard output
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94 -options boolean Prompt for standard and additional values
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95 -debug boolean Write debug output to program.dbg
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96 -verbose boolean Report some/full command line options
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97 -help boolean Report command line options and exit. More
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98 information on associated and general
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99 qualifiers can be found with -help -verbose
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100 -warning boolean Report warnings
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101 -error boolean Report errors
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102 -fatal boolean Report fatal errors
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103 -die boolean Report dying program messages
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104 -version boolean Report version number and exit
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105
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106 Input file format
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107
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108 The database definitions for following commands are available at
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109 http://soap.g-language.org/kbws/embossrc
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110
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111 gldabias reads one or more nucleotide sequences.
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112
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113 Output file format
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114
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115 The output from gldabias is to a plain text file.
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116
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117 File: nc_000913.gldabias
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118
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119 Sequence: NC_000913 LDA-BIAS: 0.742533
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120
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121
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122 Data files
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123
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124 None.
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125
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126 Notes
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127
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128 None.
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129
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130 References
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131
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132 Rocha EPC et al. (1999) "Universal replication biases in bacteria",
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133 Molecular Microbiology, 32(1):11-16
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134
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135 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
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136 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
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137 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
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138
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139 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
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140 large-scale analysis of high-throughput omics data, J. Pest Sci.,
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141 31, 7.
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142
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143 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
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144 Analysis Environment with REST and SOAP Web Service Interfaces,
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145 Nucleic Acids Res., 38, W700-W705.
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146
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147 Warnings
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148
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149 None.
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150
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151 Diagnostic Error Messages
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152
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153 None.
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154
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155 Exit status
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156
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157 It always exits with a status of 0.
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158
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159 Known bugs
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160
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161 None.
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162
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163 See also
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164
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165 gb1 Calculate strand bias of bacterial genome using B1 index
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166 gb2 Calculate strand bias of bacterial genome using B2 index
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167 gdeltagcskew Calculate strand bias of bacterial genome using delta GC skew
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168 index
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169 ggcsi GC Skew Index: an index for strand-specefic mutational bias
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170
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171 Author(s)
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172
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173 Hidetoshi Itaya (celery@g-language.org)
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174 Institute for Advanced Biosciences, Keio University
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175 252-0882 Japan
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176
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177 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
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178 Institute for Advanced Biosciences, Keio University
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179 252-0882 Japan
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180
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181 History
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182
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183 2012 - Written by Hidetoshi Itaya
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184 2013 - Fixed by Hidetoshi Itaya
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185
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186 Target users
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187
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188 This program is intended to be used by everyone and everything, from
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189 naive users to embedded scripts.
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190
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191 Comments
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192
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193 None.
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194
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