|
0
|
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
|
