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1 gaminoinfo
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2 Function
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3
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4 Prints out basic amino acid sequence statistics
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5
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6 Description
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7
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8 gaminoinfo prints out basic compositional statistics of the given amino
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9 acid sequence in a human readble manner. The calculated values are molecular
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10 weight, number of residues, average residue weight, charge, isoelectric
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11 point, number/mole/Dayhoffstat of each amino acid, and percentage of
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12 Tiny (A+C+G+S+T), Small (A+B+C+D+G+N+P+S+T+V), Aliphatic (I+L+V),
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13 Armoatic (F+H+W+Y), Non-polar (A+C+F+G+I+L+M+P+V+W+Y),
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14 Polar (D+E+H+K+N+Q+R+S+T+Z), Charged (B+D+E+H+K+R+Z), Basic (H+K+R), and
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15 Acidic (B+D+E+Z) reidues.
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16
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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 gaminoinfo
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36
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37 % gaminoinfo tsw:hbb_human
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38 Prints out basic amino acid sequence statistics
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39 AAINDEX entry output file [hbb_human.gaminoinfo]:
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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 Protein sequence(s) filename and optional
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48 format, or reference (input USA)
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49 [-outfile] outfile [*.gaminoinfo] AAINDEX entry output file
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50
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51 Additional (Optional) qualifiers: (none)
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52 Advanced (Unprompted) qualifiers: (none)
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53 Associated qualifiers:
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54
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55 "-sequence" associated qualifiers
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56 -sbegin1 integer Start of each sequence to be used
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57 -send1 integer End of each sequence to be used
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58 -sreverse1 boolean Reverse (if DNA)
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59 -sask1 boolean Ask for begin/end/reverse
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60 -snucleotide1 boolean Sequence is nucleotide
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61 -sprotein1 boolean Sequence is protein
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62 -slower1 boolean Make lower case
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63 -supper1 boolean Make upper case
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64 -scircular1 boolean Sequence is circular
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65 -sformat1 string Input sequence format
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66 -iquery1 string Input query fields or ID list
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67 -ioffset1 integer Input start position offset
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68 -sdbname1 string Database name
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69 -sid1 string Entryname
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70 -ufo1 string UFO features
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71 -fformat1 string Features format
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72 -fopenfile1 string Features file name
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73
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74 "-outfile" associated qualifiers
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75 -odirectory2 string Output directory
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76
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77 General qualifiers:
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78 -auto boolean Turn off prompts
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79 -stdout boolean Write first file to standard output
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80 -filter boolean Read first file from standard input, write
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81 first file to standard output
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82 -options boolean Prompt for standard and additional values
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83 -debug boolean Write debug output to program.dbg
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84 -verbose boolean Report some/full command line options
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85 -help boolean Report command line options and exit. More
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86 information on associated and general
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87 qualifiers can be found with -help -verbose
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88 -warning boolean Report warnings
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89 -error boolean Report errors
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90 -fatal boolean Report fatal errors
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91 -die boolean Report dying program messages
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92 -version boolean Report version number and exit
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93
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94 Input file format
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95
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96 The database definitions for following commands are available at
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97 http://soap.g-language.org/kbws/embossrc
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98
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99 gaminoinfo reads one or more protein sequences.
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100
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101 Output file format
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102
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103 The output from gaminoinfo is to a plain text file.
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104
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105 File: hbb_human.gaminoinfo
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106
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107 Sequence: P68871
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108 AminoInfo of from 1 to 158
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109
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110 Molecular weight = 19309.27 Residues = 158
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111 Average Weight = 122.21 Charge = 3.5
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112 Isoelectric Point = 7.4065
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113 Residue Number Mole% DayhoffStat
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114
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115 = 1 0.633 0.000
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116 > = 1 0.633 0.000
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117 A = Ala 16 10.127 1.178
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118 B = Asx 2 1.266 0.000
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119 C = Cys 2 1.266 0.436
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120 D = Asp 7 4.430 0.806
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121 E = Glu 8 5.063 0.844
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122 F = Phe 8 5.063 1.406
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123 G = Gly 13 8.228 0.980
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124 H = His 11 6.962 3.481
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125 K = Lys 11 6.962 1.055
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126 L = Leu 18 11.392 1.540
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127 M = Met 3 1.899 1.117
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128 N = Asn 7 4.430 1.030
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129 P = Pro 7 4.430 0.852
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130 Q = Gln 3 1.899 0.487
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131 R = Arg 3 1.899 0.387
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132 S = Ser 5 3.165 0.452
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133 T = Thr 7 4.430 0.726
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134 U = Sec 1 0.633 0.000
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135 V = Val 18 11.392 1.726
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136 W = Trp 2 1.266 0.974
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137 Y = Tyr 3 1.899 0.558
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138 _ = 1 0.633 0.000
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139
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140 Property Residues Number Mole%
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141 Tiny (A+C+G+S+T) 43 27.215
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142 Small (A+B+C+D+G+N+P+S+T+V) 84 53.165
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143 Aliphatic (I+L+V) 36 22.785
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144 Aromatic (F+H+W+Y) 24 15.190
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145 Non-polar (A+C+F+G+I+L+M+P+V+W+Y) 90 56.962
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146 Polar (D+E+H+K+N+Q+R+S+T+Z) 62 39.241
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147 Charged (B+D+E+H+K+R+Z) 42 26.582
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148 Basic (H+K+R) 25 15.823
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149 Acidic (B+D+E+Z) 17 10.759
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150
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151
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152
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153 Data files
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154
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155 None.
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156
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157 Notes
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158
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159 None.
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160
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161 References
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162
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163 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
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164 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
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165 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
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166
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167 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
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168 large-scale analysis of high-throughput omics data, J. Pest Sci.,
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169 31, 7.
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170
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171 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
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172 Analysis Environment with REST and SOAP Web Service Interfaces,
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173 Nucleic Acids Res., 38, W700-W705.
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174
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175 Warnings
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176
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177 None.
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178
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179 Diagnostic Error Messages
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180
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181 None.
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182
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183 Exit status
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184
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185 It always exits with a status of 0.
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186
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187 Known bugs
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188
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189 None.
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190
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191 See also
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192
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193 gaaui Calculates various indece of amino acid usage
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194 gcodoncompiler Calculate various kinds of amino acid and codon usage data
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195
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196 Author(s)
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197
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198 Hidetoshi Itaya (celery@g-language.org)
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199 Institute for Advanced Biosciences, Keio University
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200 252-0882 Japan
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201
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202 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
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203 Institute for Advanced Biosciences, Keio University
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204 252-0882 Japan
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205
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206 History
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207
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208 2012 - Written by Hidetoshi Itaya
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209 2013 - Fixed by Hidetoshi Itaya
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210
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211 Target users
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212
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213 This program is intended to be used by everyone and everything, from
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214 naive users to embedded scripts.
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215
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216 Comments
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217
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218 None.
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219
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