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1 gbasecounter
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2 Function
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3
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4 Creates a position weight matrix of oligomers around start codon
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5
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6 Description
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7
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8 This function creates a position weight matrix (PWM) of
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9 oligomers of specified length around the start codon of all
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10 genes in the given genome.
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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 gbasecounter
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30
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31 % gbasecounter refseqn:NC_000913
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32 Creates a position weight matrix of oligomers around start codon
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33 Weight matrix output file [nc_000913.gbasecounter]:
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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 [*.gbasecounter] Weight matrix 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 -position selection [start] Either 'start' (around start codon)
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48 or 'end' (around stop codon) to create the
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49 PWM
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50 -patlen integer [3] Length of oligomer to count (Any integer
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51 value)
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52 -upstream integer [30] Length upstream of specified position
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53 to create PWM (Any integer value)
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54 -downstream integer [30] Length downstream of specified position
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55 to create PWM (Any integer value)
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56 -[no]accid boolean [Y] Include to use sequence accession ID as
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57 query
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58
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59 Associated qualifiers:
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60
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61 "-sequence" associated qualifiers
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62 -sbegin1 integer Start of each sequence to be used
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63 -send1 integer End of each sequence to be used
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64 -sreverse1 boolean Reverse (if DNA)
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65 -sask1 boolean Ask for begin/end/reverse
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66 -snucleotide1 boolean Sequence is nucleotide
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67 -sprotein1 boolean Sequence is protein
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68 -slower1 boolean Make lower case
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69 -supper1 boolean Make upper case
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70 -scircular1 boolean Sequence is circular
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71 -sformat1 string Input sequence format
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72 -iquery1 string Input query fields or ID list
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73 -ioffset1 integer Input start position offset
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74 -sdbname1 string Database name
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75 -sid1 string Entryname
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76 -ufo1 string UFO features
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77 -fformat1 string Features format
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78 -fopenfile1 string Features file name
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79
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80 "-outfile" associated qualifiers
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81 -odirectory2 string Output directory
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82
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83 General qualifiers:
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84 -auto boolean Turn off prompts
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85 -stdout boolean Write first file to standard output
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86 -filter boolean Read first file from standard input, write
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87 first file to standard output
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88 -options boolean Prompt for standard and additional values
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89 -debug boolean Write debug output to program.dbg
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90 -verbose boolean Report some/full command line options
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91 -help boolean Report command line options and exit. More
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92 information on associated and general
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93 qualifiers can be found with -help -verbose
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94 -warning boolean Report warnings
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95 -error boolean Report errors
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96 -fatal boolean Report fatal errors
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97 -die boolean Report dying program messages
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98 -version boolean Report version number and exit
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99
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100 Input file format
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101
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102 The database definitions for following commands are available at
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103 http://soap.g-language.org/kbws/embossrc
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104
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105 gbasecounter reads one or more nucleotide sequences.
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106
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107 Output file format
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108
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109 The output from gbasecounter is to a plain text file.
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110
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111 File: nc_000913.gbasecounter
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112
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113 Sequence: NC_000913
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114 Pattern,30,29,28,27,26,25,24,23,22,21,20,19,18,17,16,15,14,13,12,11,10,9,8,7,6,5,4,3,2,1,0,-1,-2,-3,-4,-5,-6,-7,-8,-9,-10,-11,-12,-13,-14,-15,-16,-17,-18,-19,-20,-21,-22,-23,-24,-25,-26,-27,-28,-29,-30
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115 aaa,0,1,199,111,104,139,94,103,99,44,42,26,75,103,107,95,107,103,102,82,91,71,73,81,86,80,74,74,78,65,69,65,31,41,68,51,61,83,55,67,92,55,71,89,60,77,100,59,87,123,97,105,141,83,117,180,154,203,262,2,0
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116 aac,2,0,0,63,104,56,67,64,28,34,22,12,17,37,43,59,61,71,54,42,62,59,63,52,56,61,48,55,56,52,38,30,34,54,36,42,43,33,49,49,36,43,58,37,53,62,46,47,79,38,52,72,58,52,89,74,83,91,68,2,1
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117 aag,0,0,17,46,38,57,56,44,25,44,43,170,162,125,92,70,61,50,42,46,21,22,43,39,29,35,39,34,28,26,30,25,9,43,31,12,55,33,13,66,21,21,50,30,21,55,31,21,47,38,16,55,35,23,63,96,31,51,71,0,0
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118 aat,1,565,4,56,124,45,83,74,63,42,24,24,20,27,59,71,54,74,66,71,67,52,58,77,61,52,57,49,56,71,61,34,33,24,40,38,30,43,46,25,48,56,35,58,51,33,47,71,46,70,77,60,74,74,73,83,69,61,110,0,1
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119 aca,0,1,92,73,39,69,39,24,31,31,16,19,34,64,61,63,65,56,42,60,45,66,38,45,46,41,49,40,51,43,39,20,34,29,23,26,28,34,35,26,35,39,30,28,48,26,28,53,35,36,59,42,53,46,64,56,62,44,55,0,0
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120 acc,2,2,0,81,37,19,28,19,15,8,12,7,7,14,22,27,30,24,31,23,30,27,34,27,30,22,25,42,34,29,25,41,23,32,44,19,32,51,21,19,50,23,24,52,30,31,56,25,31,55,30,25,35,30,32,53,20,21,48,0,2
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121 acg,0,0,21,38,23,38,32,25,13,18,12,15,34,29,34,37,25,31,25,34,30,20,22,24,40,22,24,30,34,29,25,29,25,34,41,23,32,25,36,44,28,32,40,32,23,28,40,30,25,36,39,32,28,40,38,39,45,30,33,0,0
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122 act,0,0,1,57,35,14,30,29,21,9,6,9,9,10,17,38,28,35,30,37,41,46,38,43,39,31,31,31,30,32,27,18,55,24,20,32,16,25,32,24,31,44,14,33,43,12,35,60,24,40,58,19,36,71,22,44,46,13,45,3,1
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123
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124 [Part of this file has been deleted for brevity]
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125
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126 tcg,0.000,0.000,0.347,0.255,0.301,0.764,0.347,0.232,0.162,0.093,0.093,0.278,0.347,0.370,0.370,0.440,0.556,0.394,0.486,0.440,0.417,0.347,0.370,0.463,0.417,0.695,0.394,0.671,0.533,0.579,0.602,0.347,0.695,1.598,0.556,0.648,1.366,0.394,0.463,1.505,0.579,0.810,1.320,0.278,0.810,1.065,0.533,0.579,0.972,0.255,0.787,1.158,0.440,0.787,0.602,0.255,0.625,0.463,0.347,0.000,0.000
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127 tct,0.000,0.046,0.000,0.671,0.764,0.394,0.278,0.347,0.278,0.116,0.116,0.162,0.255,0.162,0.486,0.648,0.533,0.625,0.741,0.718,0.903,0.834,0.880,0.857,0.741,0.857,0.671,0.648,0.857,0.695,0.625,0.440,0.880,0.463,0.556,1.111,0.509,0.579,1.227,0.556,0.370,1.135,0.671,0.648,1.250,0.834,0.509,1.273,0.440,0.718,0.972,1.042,0.648,0.926,0.533,0.625,0.556,0.185,1.690,0.000,0.000
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128 tga,0.000,0.000,2.315,0.463,1.227,1.297,1.088,0.949,0.625,0.417,1.065,0.903,1.737,1.667,1.042,1.158,1.366,1.320,1.227,1.158,0.926,1.459,1.181,0.810,1.366,0.972,0.972,1.111,0.764,0.787,1.227,0.000,1.598,1.250,0.000,1.482,1.181,0.000,1.459,1.389,0.000,1.783,1.297,0.000,1.505,1.482,0.023,1.343,1.690,0.000,1.690,1.204,0.000,1.389,0.949,0.000,2.408,0.996,0.000,0.023,24.311
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129 tgc,0.023,0.000,0.000,0.394,0.996,0.579,0.787,0.556,0.208,0.185,0.208,0.116,0.278,0.324,0.394,0.834,0.486,0.394,0.718,0.556,0.509,0.857,0.509,0.625,0.810,0.741,0.695,0.834,0.625,0.787,1.158,0.347,1.158,1.621,0.394,1.667,1.204,0.347,1.551,1.320,0.417,1.088,1.065,0.232,1.320,1.042,0.139,1.204,0.996,0.208,0.996,0.602,0.139,0.648,0.764,0.069,0.857,0.394,0.023,0.000,7.803
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130 tgg,0.000,0.023,0.069,0.208,0.370,0.509,0.486,0.417,0.394,0.671,1.343,1.713,1.621,1.482,0.810,0.834,0.718,0.301,0.463,0.509,0.509,0.741,0.579,0.509,0.625,0.486,0.509,0.625,0.625,0.533,0.857,0.996,0.718,1.968,1.042,0.880,1.760,0.671,0.949,1.459,0.556,0.787,0.903,0.718,0.695,1.273,0.533,0.440,0.648,0.880,0.417,0.718,0.648,0.278,0.625,0.463,0.440,0.486,0.116,0.023,11.021
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131 tgt,0.023,0.880,0.023,0.533,1.135,0.301,0.440,0.602,0.417,0.208,0.232,0.185,0.185,0.278,0.370,0.440,0.533,0.556,0.648,0.764,0.509,0.926,0.579,0.718,0.880,0.695,0.718,0.741,0.741,0.579,0.625,0.278,1.158,0.857,0.278,0.972,0.718,0.324,0.926,0.695,0.463,1.111,0.834,0.162,1.482,0.787,0.278,1.065,0.695,0.278,1.042,0.695,0.208,0.903,0.718,0.139,0.857,0.232,0.093,0.023,7.340
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132 tta,0.000,0.000,6.506,0.648,0.810,1.829,1.320,0.602,0.486,0.509,0.255,0.347,0.301,0.834,1.320,1.459,1.412,1.667,1.644,1.852,1.667,1.574,1.366,1.042,1.204,1.621,1.505,1.227,1.436,1.088,1.273,1.343,0.486,1.158,1.042,0.440,1.135,1.389,0.370,1.273,1.574,0.486,1.875,1.505,0.463,1.991,1.875,0.533,2.362,2.061,0.324,2.084,2.200,0.509,1.505,1.320,0.463,1.366,0.648,0.000,0.069
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133 ttc,0.000,0.000,0.000,0.648,0.417,0.695,0.764,0.347,0.301,0.278,0.208,0.023,0.232,0.533,0.718,0.718,0.903,1.042,1.158,0.880,1.158,1.065,0.903,0.834,1.343,0.996,0.926,0.810,0.741,0.834,1.042,0.926,0.579,1.088,0.695,0.695,1.297,0.741,0.741,1.111,0.926,0.787,1.366,0.695,0.857,1.412,0.648,0.834,1.111,0.440,0.602,1.250,1.019,1.135,0.787,0.440,0.880,0.509,0.370,0.000,0.000
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134 ttg,0.857,0.023,0.255,0.394,0.556,1.111,0.533,0.463,0.417,0.185,0.232,0.533,0.602,1.042,0.718,0.695,1.135,0.972,0.857,0.926,0.787,0.671,1.320,0.695,0.903,1.204,0.880,0.764,0.926,0.741,0.718,1.019,0.347,1.551,1.042,0.370,2.014,0.834,0.463,2.061,0.880,0.278,2.014,0.857,0.208,2.593,0.741,0.278,1.922,0.764,0.417,2.130,0.834,0.208,1.111,0.394,0.093,1.111,0.417,0.000,0.023
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135 ttt,0.023,0.440,0.093,1.598,1.181,1.320,1.829,1.343,0.648,0.370,0.394,0.278,0.185,0.440,1.135,1.574,1.667,1.945,2.315,2.362,2.431,2.501,2.107,2.362,1.806,2.014,2.292,2.014,1.598,1.760,1.829,1.389,1.505,1.042,1.343,1.297,0.926,1.528,1.574,1.227,1.482,1.737,1.389,1.667,1.922,1.389,1.945,1.922,1.343,1.806,1.760,1.389,2.014,1.760,1.065,0.949,1.111,0.625,1.227,0.023,0.023
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136
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137
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138 Data files
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139
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140 None.
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141
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142 Notes
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143
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144 None.
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145
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146 References
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147
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148 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
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149 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
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150 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
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151
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152 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
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153 large-scale analysis of high-throughput omics data, J. Pest Sci.,
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154 31, 7.
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155
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156 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
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157 Analysis Environment with REST and SOAP Web Service Interfaces,
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158 Nucleic Acids Res., 38, W700-W705.
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159
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160 Warnings
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161
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162 None.
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163
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164 Diagnostic Error Messages
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165
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166 None.
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167
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168 Exit status
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169
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170 It always exits with a status of 0.
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171
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172 Known bugs
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173
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174 None.
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175
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176 See also
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177
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178 gbasezvalue Extracts conserved oligomers per position using Z-score
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179 gviewcds Displays a graph of nucleotide contents around start and stop
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180 codons
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181
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182 Author(s)
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183
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184 Hidetoshi Itaya (celery@g-language.org)
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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 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
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189 Institute for Advanced Biosciences, Keio University
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190 252-0882 Japan
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191
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192 History
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193
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194 2012 - Written by Hidetoshi Itaya
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195 2013 - Fixed by Hidetoshi Itaya
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196
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197 Target users
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198
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199 This program is intended to be used by everyone and everything, from
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200 naive users to embedded scripts.
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201
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202 Comments
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203
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204 None.
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205
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