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1 gb1
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2 Function
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3
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4 Calculate strand bias of bacterial genome using B1 index
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5
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6 Description
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7
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8 gb1 calculates the strand bias of bacterial genome using B1 index,
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9 first proposed by Lobry and Sueoka (2002), and further extended by
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10 Rocha et al. (2006). Basic idea of B1 index is to calculate the
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11 distance between the two strands, when the leading and lagging strands
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12 are plotted in a coordinate system with axes representing G/(G+C) and
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13 A/(A+T), using the third codon position of genes. This index measures the
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14 degree of replication-induced bias from Chargaff's second parity rule.
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15 Rocha et al. modified B1 index to only use >fourfold degenerate codons,
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16 and to use T/(A+T) in place of A/(A+T).
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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 gb1
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36
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37 % gb1 refseqn:NC_000913
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38 Calculate strand bias of bacterial genome using B1 index
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39 Program compseq output file [nc_000913.gb1]:
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40
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41 Go to the input files for this example
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42 Go to the output files for this example
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43
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44 Command line arguments
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45
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46 Standard (Mandatory) qualifiers:
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47 [-sequence] seqall Nucleotide sequence(s) filename and optional
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48 format, or reference (input USA)
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49 [-outfile] outfile [*.gb1] Program compseq output file
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50
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51 Additional (Optional) qualifiers: (none)
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52 Advanced (Unprompted) qualifiers:
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53 -method selection [rocha] Choose method of 'lobry' or 'rocha'
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54 -[no]accid boolean [Y] Include to use sequence accession ID as
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55 query
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56
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57 Associated qualifiers:
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58
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59 "-sequence" associated qualifiers
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60 -sbegin1 integer Start of each sequence to be used
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61 -send1 integer End of each sequence to be used
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62 -sreverse1 boolean Reverse (if DNA)
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63 -sask1 boolean Ask for begin/end/reverse
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64 -snucleotide1 boolean Sequence is nucleotide
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65 -sprotein1 boolean Sequence is protein
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66 -slower1 boolean Make lower case
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67 -supper1 boolean Make upper case
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68 -scircular1 boolean Sequence is circular
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69 -sformat1 string Input sequence format
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70 -iquery1 string Input query fields or ID list
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71 -ioffset1 integer Input start position offset
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72 -sdbname1 string Database name
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73 -sid1 string Entryname
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74 -ufo1 string UFO features
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75 -fformat1 string Features format
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76 -fopenfile1 string Features file name
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77
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78 "-outfile" associated qualifiers
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79 -odirectory2 string Output directory
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80
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81 General qualifiers:
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82 -auto boolean Turn off prompts
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83 -stdout boolean Write first file to standard output
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84 -filter boolean Read first file from standard input, write
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85 first file to standard output
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86 -options boolean Prompt for standard and additional values
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87 -debug boolean Write debug output to program.dbg
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88 -verbose boolean Report some/full command line options
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89 -help boolean Report command line options and exit. More
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90 information on associated and general
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91 qualifiers can be found with -help -verbose
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92 -warning boolean Report warnings
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93 -error boolean Report errors
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94 -fatal boolean Report fatal errors
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95 -die boolean Report dying program messages
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96 -version boolean Report version number and exit
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97
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98 Input file format
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99
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100 The database definitions for following commands are available at
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101 http://soap.g-language.org/kbws/embossrc
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102
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103 gb1 reads one or more nucleotide sequences.
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104
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105 Output file format
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106
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107 The output from gb1 is to a plain text file.
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108
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109 File: nc_000913.gb1
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110
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111 Sequence: NC_000913 B1: 0.0630702874711314
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112
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113
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114 Data files
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115
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116 None.
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117
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118 Notes
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119
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120 None.
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121
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122 References
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123
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124 Lobry JR and Sueoka N (2002) Asymmetric directional mutation pressures in
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125 bacteria, Genome Biology, 3(10):0058
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126
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127 Rocha EPC et al. (2006) Similar compositional biases are caused by very
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128 different mutational effects, Genome Research, 16:1537-1547
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129
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130 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
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131 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
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132 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
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133
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134 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
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135 large-scale analysis of high-throughput omics data, J. Pest Sci.,
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136 31, 7.
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137
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138 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
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139 Analysis Environment with REST and SOAP Web Service Interfaces,
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140 Nucleic Acids Res., 38, W700-W705.
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141
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142 Warnings
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143
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144 None.
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145
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146 Diagnostic Error Messages
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147
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148 None.
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149
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150 Exit status
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151
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152 It always exits with a status of 0.
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153
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154 Known bugs
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155
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156 None.
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157
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158 See also
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159
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160 gb2 Calculate strand bias of bacterial genome using B2 index
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161 gdeltagcskew Calculate strand bias of bacterial genome using delta GC skew
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162 index
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163 ggcsi GC Skew Index: an index for strand-specefic mutational bias
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164 gldabias Calculate strand bias of bacterial genome using linear
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165 discriminant analysis (LDA)
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166
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167 Author(s)
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168
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169 Hidetoshi Itaya (celery@g-language.org)
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170 Institute for Advanced Biosciences, Keio University
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171 252-0882 Japan
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172
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173 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
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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 History
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178
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179 2012 - Written by Hidetoshi Itaya
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180 2013 - Fixed by Hidetoshi Itaya
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181
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182 Target users
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183
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184 This program is intended to be used by everyone and everything, from
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185 naive users to embedded scripts.
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186
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187 Comments
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188
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189 None.
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190
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