Mercurial > repos > ktnyt > gembassy
comparison GEMBASSY-1.0.3/doc/text/gbaseinformationcontent.txt @ 0:8300eb051bea draft
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author | ktnyt |
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date | Fri, 26 Jun 2015 05:19:29 -0400 |
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1 gbaseinformationcontent | |
2 Function | |
3 | |
4 Calculates and graphs the sequence conservation using information content | |
5 | |
6 Description | |
7 | |
8 This function calculates and graphs the sequence conservation in regions | |
9 around the start/stop codons using information content. Values are obtained | |
10 by subtracting the entropy for each positfion from the maximum possible | |
11 value (which will be 2 in the case of nucleotide sequences). Information | |
12 content will show the highest value when the frequency is most biased to a | |
13 single alphabet. | |
14 | |
15 Information content I is obtained by subtracting the entropy H from the | |
16 maximum uncertainty log(2,|M|): | |
17 I(P(i)) = log(2,|M|) - (-sum(P(i,j) * log(2,P(i,j)))) | |
18 | |
19 G-language SOAP service is provided by the | |
20 Institute for Advanced Biosciences, Keio University. | |
21 The original web service is located at the following URL: | |
22 | |
23 http://www.g-language.org/wiki/soap | |
24 | |
25 WSDL(RPC/Encoded) file is located at: | |
26 | |
27 http://soap.g-language.org/g-language.wsdl | |
28 | |
29 Documentation on G-language Genome Analysis Environment methods are | |
30 provided at the Document Center | |
31 | |
32 http://ws.g-language.org/gdoc/ | |
33 | |
34 Usage | |
35 | |
36 Here is a sample session with gbaseinformationcontent | |
37 | |
38 % gbaseinformationcontent refseqn:NC_000913 | |
39 Calculates and graphs the sequence conservation using information content | |
40 Program compseq output file (optional) [nc_000913.gbaseinformationcontent]: | |
41 | |
42 Go to the input files for this example | |
43 Go to the output files for this example | |
44 | |
45 Example 2 | |
46 | |
47 % gbaseinformationcontent refseqn:NC_000913 -plot -graph png | |
48 Calculates and graphs the sequence conservation using information content | |
49 Created gbaseinformationcontent.1.png | |
50 | |
51 Go to the input files for this example | |
52 Go to the output files for this example | |
53 | |
54 Command line arguments | |
55 | |
56 Standard (Mandatory) qualifiers (* if not always prompted): | |
57 [-sequence] seqall Nucleotide sequence(s) filename and optional | |
58 format, or reference (input USA) | |
59 * -graph xygraph [$EMBOSS_GRAPHICS value, or x11] Graph type | |
60 (ps, hpgl, hp7470, hp7580, meta, cps, x11, | |
61 tek, tekt, none, data, xterm, png, gif, svg) | |
62 * -outfile outfile [*.gbaseinformationcontent] Program compseq | |
63 output file (optional) | |
64 | |
65 Additional (Optional) qualifiers: (none) | |
66 Advanced (Unprompted) qualifiers: | |
67 -position selection [start] Either 'start' (around start codon) | |
68 or 'end' (around stop codon) to create the | |
69 PWM | |
70 -upstream integer [30] Length upstream of specified position | |
71 to create PWM (Any integer value) | |
72 -downstream integer [30] Length downstream of specified position | |
73 to create PWM (Any integer value) | |
74 -patlen integer [3] Length of oligomer to count (Any integer | |
75 value) | |
76 -[no]accid boolean [Y] Include to use sequence accession ID as | |
77 query | |
78 -plot toggle [N] Include to plot result | |
79 | |
80 Associated qualifiers: | |
81 | |
82 "-sequence" associated qualifiers | |
83 -sbegin1 integer Start of each sequence to be used | |
84 -send1 integer End of each sequence to be used | |
85 -sreverse1 boolean Reverse (if DNA) | |
86 -sask1 boolean Ask for begin/end/reverse | |
87 -snucleotide1 boolean Sequence is nucleotide | |
88 -sprotein1 boolean Sequence is protein | |
89 -slower1 boolean Make lower case | |
90 -supper1 boolean Make upper case | |
91 -scircular1 boolean Sequence is circular | |
92 -sformat1 string Input sequence format | |
93 -iquery1 string Input query fields or ID list | |
94 -ioffset1 integer Input start position offset | |
95 -sdbname1 string Database name | |
96 -sid1 string Entryname | |
97 -ufo1 string UFO features | |
98 -fformat1 string Features format | |
99 -fopenfile1 string Features file name | |
100 | |
101 "-graph" associated qualifiers | |
102 -gprompt boolean Graph prompting | |
103 -gdesc string Graph description | |
104 -gtitle string Graph title | |
105 -gsubtitle string Graph subtitle | |
106 -gxtitle string Graph x axis title | |
107 -gytitle string Graph y axis title | |
108 -goutfile string Output file for non interactive displays | |
109 -gdirectory string Output directory | |
110 | |
111 "-outfile" associated qualifiers | |
112 -odirectory string Output directory | |
113 | |
114 General qualifiers: | |
115 -auto boolean Turn off prompts | |
116 -stdout boolean Write first file to standard output | |
117 -filter boolean Read first file from standard input, write | |
118 first file to standard output | |
119 -options boolean Prompt for standard and additional values | |
120 -debug boolean Write debug output to program.dbg | |
121 -verbose boolean Report some/full command line options | |
122 -help boolean Report command line options and exit. More | |
123 information on associated and general | |
124 qualifiers can be found with -help -verbose | |
125 -warning boolean Report warnings | |
126 -error boolean Report errors | |
127 -fatal boolean Report fatal errors | |
128 -die boolean Report dying program messages | |
129 -version boolean Report version number and exit | |
130 | |
131 Input file format | |
132 | |
133 The database definitions for following commands are available at | |
134 http://soap.g-language.org/kbws/embossrc | |
135 | |
136 gbaseinformationcontent reads one or more nucleotide sequences. | |
137 | |
138 Output file format | |
139 | |
140 The output from gbaseinformationcontent is to a plain text file or the | |
141 EMBOSS graphics device. | |
142 | |
143 File: nc_000913.gbaseinformationcontent | |
144 | |
145 Sequence: NC_000913 | |
146 -30,2.42457 | |
147 -29,2.42811 | |
148 -28,2.43235 | |
149 -27,2.43116 | |
150 -26,2.44278 | |
151 -25,2.44236 | |
152 -24,2.44502 | |
153 -23,2.46097 | |
154 -22,2.46588 | |
155 | |
156 [Part of this file has been deleted for brevity] | |
157 | |
158 21,2.27547 | |
159 22,2.46974 | |
160 23,2.46342 | |
161 24,2.32686 | |
162 25,2.46245 | |
163 26,2.46061 | |
164 27,2.27664 | |
165 28,2.45650 | |
166 29,2.48206 | |
167 30,2.29140 | |
168 | |
169 | |
170 Data files | |
171 | |
172 None. | |
173 | |
174 Notes | |
175 | |
176 None. | |
177 | |
178 References | |
179 | |
180 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and | |
181 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench | |
182 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. | |
183 | |
184 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for | |
185 large-scale analysis of high-throughput omics data, J. Pest Sci., | |
186 31, 7. | |
187 | |
188 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome | |
189 Analysis Environment with REST and SOAP Web Service Interfaces, | |
190 Nucleic Acids Res., 38, W700-W705. | |
191 | |
192 Warnings | |
193 | |
194 None. | |
195 | |
196 Diagnostic Error Messages | |
197 | |
198 None. | |
199 | |
200 Exit status | |
201 | |
202 It always exits with a status of 0. | |
203 | |
204 Known bugs | |
205 | |
206 None. | |
207 | |
208 See also | |
209 | |
210 gbaseentropy Calculates and graphs the sequence conservation | |
211 using Shanon uncertainty (entropy) | |
212 gbaserelativeentropy Calculates and graphs the sequence conservation | |
213 using Kullback-Leibler divergence (relative | |
214 entropy) | |
215 | |
216 Author(s) | |
217 | |
218 Hidetoshi Itaya (celery@g-language.org) | |
219 Institute for Advanced Biosciences, Keio University | |
220 252-0882 Japan | |
221 | |
222 Kazuharu Arakawa (gaou@sfc.keio.ac.jp) | |
223 Institute for Advanced Biosciences, Keio University | |
224 252-0882 Japan | |
225 | |
226 History | |
227 | |
228 2012 - Written by Hidetoshi Itaya | |
229 2013 - Fixed by Hidetoshi Itaya | |
230 | |
231 Target users | |
232 | |
233 This program is intended to be used by everyone and everything, from | |
234 naive users to embedded scripts. | |
235 | |
236 Comments | |
237 | |
238 None. | |
239 |