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comparison GEMBASSY-1.0.3/doc/text/gaminoinfo.txt @ 0:8300eb051bea draft

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1 gaminoinfo
2 Function
3
4 Prints out basic amino acid sequence statistics
5
6 Description
7
8 gaminoinfo prints out basic compositional statistics of the given amino
9 acid sequence in a human readble manner. The calculated values are molecular
10 weight, number of residues, average residue weight, charge, isoelectric
11 point, number/mole/Dayhoffstat of each amino acid, and percentage of
12 Tiny (A+C+G+S+T), Small (A+B+C+D+G+N+P+S+T+V), Aliphatic (I+L+V),
13 Armoatic (F+H+W+Y), Non-polar (A+C+F+G+I+L+M+P+V+W+Y),
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
15 Acidic (B+D+E+Z) reidues.
16
17
18 G-language SOAP service is provided by the
19 Institute for Advanced Biosciences, Keio University.
20 The original web service is located at the following URL:
21
22 http://www.g-language.org/wiki/soap
23
24 WSDL(RPC/Encoded) file is located at:
25
26 http://soap.g-language.org/g-language.wsdl
27
28 Documentation on G-language Genome Analysis Environment methods are
29 provided at the Document Center
30
31 http://ws.g-language.org/gdoc/
32
33 Usage
34
35 Here is a sample session with gaminoinfo
36
37 % gaminoinfo tsw:hbb_human
38 Prints out basic amino acid sequence statistics
39 AAINDEX entry output file [hbb_human.gaminoinfo]:
40
41 Go to the input files for this example
42 Go to the output files for this example
43
44 Command line arguments
45
46 Standard (Mandatory) qualifiers:
47 [-sequence] seqall Protein sequence(s) filename and optional
48 format, or reference (input USA)
49 [-outfile] outfile [*.gaminoinfo] AAINDEX entry output file
50
51 Additional (Optional) qualifiers: (none)
52 Advanced (Unprompted) qualifiers: (none)
53 Associated qualifiers:
54
55 "-sequence" associated qualifiers
56 -sbegin1 integer Start of each sequence to be used
57 -send1 integer End of each sequence to be used
58 -sreverse1 boolean Reverse (if DNA)
59 -sask1 boolean Ask for begin/end/reverse
60 -snucleotide1 boolean Sequence is nucleotide
61 -sprotein1 boolean Sequence is protein
62 -slower1 boolean Make lower case
63 -supper1 boolean Make upper case
64 -scircular1 boolean Sequence is circular
65 -sformat1 string Input sequence format
66 -iquery1 string Input query fields or ID list
67 -ioffset1 integer Input start position offset
68 -sdbname1 string Database name
69 -sid1 string Entryname
70 -ufo1 string UFO features
71 -fformat1 string Features format
72 -fopenfile1 string Features file name
73
74 "-outfile" associated qualifiers
75 -odirectory2 string Output directory
76
77 General qualifiers:
78 -auto boolean Turn off prompts
79 -stdout boolean Write first file to standard output
80 -filter boolean Read first file from standard input, write
81 first file to standard output
82 -options boolean Prompt for standard and additional values
83 -debug boolean Write debug output to program.dbg
84 -verbose boolean Report some/full command line options
85 -help boolean Report command line options and exit. More
86 information on associated and general
87 qualifiers can be found with -help -verbose
88 -warning boolean Report warnings
89 -error boolean Report errors
90 -fatal boolean Report fatal errors
91 -die boolean Report dying program messages
92 -version boolean Report version number and exit
93
94 Input file format
95
96 The database definitions for following commands are available at
97 http://soap.g-language.org/kbws/embossrc
98
99 gaminoinfo reads one or more protein sequences.
100
101 Output file format
102
103 The output from gaminoinfo is to a plain text file.
104
105 File: hbb_human.gaminoinfo
106
107 Sequence: P68871
108 AminoInfo of from 1 to 158
109
110 Molecular weight = 19309.27 Residues = 158
111 Average Weight = 122.21 Charge = 3.5
112 Isoelectric Point = 7.4065
113 Residue Number Mole% DayhoffStat
114
115 = 1 0.633 0.000
116 > = 1 0.633 0.000
117 A = Ala 16 10.127 1.178
118 B = Asx 2 1.266 0.000
119 C = Cys 2 1.266 0.436
120 D = Asp 7 4.430 0.806
121 E = Glu 8 5.063 0.844
122 F = Phe 8 5.063 1.406
123 G = Gly 13 8.228 0.980
124 H = His 11 6.962 3.481
125 K = Lys 11 6.962 1.055
126 L = Leu 18 11.392 1.540
127 M = Met 3 1.899 1.117
128 N = Asn 7 4.430 1.030
129 P = Pro 7 4.430 0.852
130 Q = Gln 3 1.899 0.487
131 R = Arg 3 1.899 0.387
132 S = Ser 5 3.165 0.452
133 T = Thr 7 4.430 0.726
134 U = Sec 1 0.633 0.000
135 V = Val 18 11.392 1.726
136 W = Trp 2 1.266 0.974
137 Y = Tyr 3 1.899 0.558
138 _ = 1 0.633 0.000
139
140 Property Residues Number Mole%
141 Tiny (A+C+G+S+T) 43 27.215
142 Small (A+B+C+D+G+N+P+S+T+V) 84 53.165
143 Aliphatic (I+L+V) 36 22.785
144 Aromatic (F+H+W+Y) 24 15.190
145 Non-polar (A+C+F+G+I+L+M+P+V+W+Y) 90 56.962
146 Polar (D+E+H+K+N+Q+R+S+T+Z) 62 39.241
147 Charged (B+D+E+H+K+R+Z) 42 26.582
148 Basic (H+K+R) 25 15.823
149 Acidic (B+D+E+Z) 17 10.759
150
151
152
153 Data files
154
155 None.
156
157 Notes
158
159 None.
160
161 References
162
163 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
164 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
165 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
166
167 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
168 large-scale analysis of high-throughput omics data, J. Pest Sci.,
169 31, 7.
170
171 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
172 Analysis Environment with REST and SOAP Web Service Interfaces,
173 Nucleic Acids Res., 38, W700-W705.
174
175 Warnings
176
177 None.
178
179 Diagnostic Error Messages
180
181 None.
182
183 Exit status
184
185 It always exits with a status of 0.
186
187 Known bugs
188
189 None.
190
191 See also
192
193 gaaui Calculates various indece of amino acid usage
194 gcodoncompiler Calculate various kinds of amino acid and codon usage data
195
196 Author(s)
197
198 Hidetoshi Itaya (celery@g-language.org)
199 Institute for Advanced Biosciences, Keio University
200 252-0882 Japan
201
202 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
203 Institute for Advanced Biosciences, Keio University
204 252-0882 Japan
205
206 History
207
208 2012 - Written by Hidetoshi Itaya
209 2013 - Fixed by Hidetoshi Itaya
210
211 Target users
212
213 This program is intended to be used by everyone and everything, from
214 naive users to embedded scripts.
215
216 Comments
217
218 None.
219