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comparison GEMBASSY-1.0.3/doc/text/gbaserelativeentropy.txt @ 2:8947fca5f715 draft default tip
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author | ktnyt |
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date | Fri, 26 Jun 2015 05:21:44 -0400 |
parents | 84a17b3fad1f |
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1 gbaserelativeentropy | |
2 Function | |
3 | |
4 Calculates and graphs the sequence conservation using Kullback-Leibler | |
5 | |
6 Description | |
7 | |
8 This function calculates and graphs the sequence conservation in regions | |
9 around the start/stop codons using Kullback-Leibler divergence (relative | |
10 entropy). In realistic conditions, as background nucleotide composition | |
11 (e.g. G+C content) varies among species. Kullback-Leibler divergence | |
12 calculates the entropy with reduced background noise. | |
13 | |
14 The relative entropy H at position i with distribution P(i) is calculated | |
15 as follows: | |
16 H(P(i)||pi) = sum(P(i,j) * log(2, P(i,j)/pi(j))) | |
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 gbaserelativeentropy | |
36 | |
37 % gbaserelativeentropy refseqn:NC_000913 | |
38 Calculates and graphs the sequence conservation using Kullback-Leibler | |
39 divergence (relative entropy) | |
40 Program compseq output file (optional) [nc_000913.gbaserelativeentropy]: | |
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 % gbaserelativeentropy refseqn:NC_000913 -plot -graph png | |
48 Calculates and graphs the sequence conservation using Kullback-Leibler | |
49 divergence (relative entropy) | |
50 Created gbaserelativeentropy.1.png | |
51 | |
52 Go to the input files for this example | |
53 Go to the output files for this example | |
54 | |
55 Command line arguments | |
56 | |
57 Calculates and graphs the sequence conservation using Kullback-Leibler | |
58 divergence (relative entropy) | |
59 Version: EMBOSS:6.5.7.0 GEMBASSY:1.0.1 | |
60 | |
61 Standard (Mandatory) qualifiers (* if not always prompted): | |
62 [-sequence] seqall Nucleotide sequence(s) filename and optional | |
63 format, or reference (input USA) | |
64 * -graph xygraph [$EMBOSS_GRAPHICS value, or x11] Graph type | |
65 (ps, hpgl, hp7470, hp7580, meta, cps, x11, | |
66 tek, tekt, none, data, xterm, png, gif, svg) | |
67 * -outfile outfile [*.gbaserelativeentropy] Program compseq | |
68 output file (optional) | |
69 | |
70 Additional (Optional) qualifiers: (none) | |
71 Advanced (Unprompted) qualifiers: | |
72 -position selection [start] Either 'start' (around start codon) | |
73 or 'end' (around stop codon) to create the | |
74 PWM | |
75 -patlen integer [3] Length of oligomer to count (Any integer | |
76 value) | |
77 -upstream integer [30] Length upstream of specified position | |
78 to create PWM (Any integer value) | |
79 -downstream integer [30] Length downstream of specified position | |
80 to create PWM (Any integer value) | |
81 -[no]accid boolean [Y] Include to use sequence accession ID as | |
82 query | |
83 -plot toggle [N] Include to plot result | |
84 | |
85 Associated qualifiers: | |
86 | |
87 "-sequence" associated qualifiers | |
88 -sbegin1 integer Start of each sequence to be used | |
89 -send1 integer End of each sequence to be used | |
90 -sreverse1 boolean Reverse (if DNA) | |
91 -sask1 boolean Ask for begin/end/reverse | |
92 -snucleotide1 boolean Sequence is nucleotide | |
93 -sprotein1 boolean Sequence is protein | |
94 -slower1 boolean Make lower case | |
95 -supper1 boolean Make upper case | |
96 -scircular1 boolean Sequence is circular | |
97 -sformat1 string Input sequence format | |
98 -iquery1 string Input query fields or ID list | |
99 -ioffset1 integer Input start position offset | |
100 -sdbname1 string Database name | |
101 -sid1 string Entryname | |
102 -ufo1 string UFO features | |
103 -fformat1 string Features format | |
104 -fopenfile1 string Features file name | |
105 | |
106 "-graph" associated qualifiers | |
107 -gprompt boolean Graph prompting | |
108 -gdesc string Graph description | |
109 -gtitle string Graph title | |
110 -gsubtitle string Graph subtitle | |
111 -gxtitle string Graph x axis title | |
112 -gytitle string Graph y axis title | |
113 -goutfile string Output file for non interactive displays | |
114 -gdirectory string Output directory | |
115 | |
116 "-outfile" associated qualifiers | |
117 -odirectory string Output directory | |
118 | |
119 General qualifiers: | |
120 -auto boolean Turn off prompts | |
121 -stdout boolean Write first file to standard output | |
122 -filter boolean Read first file from standard input, write | |
123 first file to standard output | |
124 -options boolean Prompt for standard and additional values | |
125 -debug boolean Write debug output to program.dbg | |
126 -verbose boolean Report some/full command line options | |
127 -help boolean Report command line options and exit. More | |
128 information on associated and general | |
129 qualifiers can be found with -help -verbose | |
130 -warning boolean Report warnings | |
131 -error boolean Report errors | |
132 -fatal boolean Report fatal errors | |
133 -die boolean Report dying program messages | |
134 -version boolean Report version number and exit | |
135 | |
136 Input file format | |
137 | |
138 The database definitions for following commands are available at | |
139 http://soap.g-language.org/kbws/embossrc | |
140 | |
141 gbaserelativeentropy reads one or more nucleotide sequences. | |
142 | |
143 Output file format | |
144 | |
145 The output from gbaserelativeentropy is to a plain text file or the | |
146 EMBOSS graphics device. | |
147 | |
148 File: nc_000913.gbaserelativeentropy | |
149 | |
150 Sequence: NC_000913 | |
151 -30,-0.46682 | |
152 -29,-0.46265 | |
153 -28,-0.45732 | |
154 -27,-0.45704 | |
155 -26,-0.44692 | |
156 -25,-0.44396 | |
157 -24,-0.43528 | |
158 -23,-0.43419 | |
159 -22,-0.42518 | |
160 | |
161 [Part of this file has been deleted for brevity] | |
162 | |
163 21,-0.40010 | |
164 22,-0.41772 | |
165 23,-0.42503 | |
166 24,-0.39675 | |
167 25,-0.43091 | |
168 26,-0.43196 | |
169 27,-0.40576 | |
170 28,-0.43387 | |
171 29,-0.41228 | |
172 30,-0.38869 | |
173 | |
174 | |
175 Data files | |
176 | |
177 None. | |
178 | |
179 Notes | |
180 | |
181 None. | |
182 | |
183 References | |
184 | |
185 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and | |
186 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench | |
187 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. | |
188 | |
189 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for | |
190 large-scale analysis of high-throughput omics data, J. Pest Sci., | |
191 31, 7. | |
192 | |
193 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome | |
194 Analysis Environment with REST and SOAP Web Service Interfaces, | |
195 Nucleic Acids Res., 38, W700-W705. | |
196 | |
197 Warnings | |
198 | |
199 None. | |
200 | |
201 Diagnostic Error Messages | |
202 | |
203 None. | |
204 | |
205 Exit status | |
206 | |
207 It always exits with a status of 0. | |
208 | |
209 Known bugs | |
210 | |
211 None. | |
212 | |
213 See also | |
214 | |
215 gbase_entropy Calculates and graphs the sequence conservation | |
216 using Shanon uncertainty (entropy) | |
217 gbase_information_content Calculates and graphs the sequence conservation | |
218 using information content | |
219 | |
220 Author(s) | |
221 | |
222 Hidetoshi Itaya (celery@g-language.org) | |
223 Institute for Advanced Biosciences, Keio University | |
224 252-0882 Japan | |
225 | |
226 Kazuharu Arakawa (gaou@sfc.keio.ac.jp) | |
227 Institute for Advanced Biosciences, Keio University | |
228 252-0882 Japan | |
229 | |
230 History | |
231 | |
232 2012 - Written by Hidetoshi Itaya | |
233 2013 - Fixed by Hidetoshi Itaya | |
234 | |
235 Target users | |
236 | |
237 This program is intended to be used by everyone and everything, from | |
238 naive users to embedded scripts. | |
239 | |
240 Comments | |
241 | |
242 None. | |
243 |