Mercurial > repos > ktnyt > gembassy

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Initial upload
author ktnyt
date Fri, 26 Jun 2015 05:19:29 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:8300eb051bea
1 ggcskew
2 Function
3
4 Calculates the GC skew of the input sequence
5
6 Description
7
8 ggcskew calculates and plots the GC skew of the given sequence. The "skew"
9 of a sequence is calculated as (C-G)/(C+G) in GC skew. The program can
10 alternatively calculate AT skew, purine skew, and keto skew, as well as
11 cumulative skew. GC skew is used to observe various biological aspects
12 such as prediction of replication origin and terminus in bacteria.
13
14 G-language SOAP service is provided by the
15 Institute for Advanced Biosciences, Keio University.
16 The original web service is located at the following URL:
17
18 http://www.g-language.org/wiki/soap
19
20 WSDL(RPC/Encoded) file is located at:
21
22 http://soap.g-language.org/g-language.wsdl
23
24 Documentation on G-language Genome Analysis Environment methods are
25 provided at the Document Center
26
27 http://ws.g-language.org/gdoc/
28
29 Usage
30
31 Here is a sample session with ggcskew
32
33 % ggcskew refseqn:NC_000913
34 Calculates the GC skew of the input sequence
35 Program compseq output file (optional) [nc_000913.ggcskew]:
36
37 Go to the input files for this example
38 Go to the output files for this example
39
40 Example 2
41
42 % ggcskew refseqn:NC_000913 -plot -graph png
43 Calculates the GC skew of the input sequence
44 Created ggcskew.1.png
45
46 Go to the input files for this example
47 Go to the output files for this example
48
49 Command line arguments
50
51 Standard (Mandatory) qualifiers (* if not always prompted):
52 [-sequence] seqall Nucleotide sequence(s) filename and optional
53 format, or reference (input USA)
54 * -graph xygraph [$EMBOSS_GRAPHICS value, or x11] Graph type
55 (ps, hpgl, hp7470, hp7580, meta, cps, x11,
56 tek, tekt, none, data, xterm, png, gif, svg)
57 * -outfile outfile [*.ggcskew] Program compseq output file
58 (optional)
59
60 Additional (Optional) qualifiers: (none)
61 Advanced (Unprompted) qualifiers:
62 -window integer [10000] Window size to observe (Any integer
63 value)
64 -slide integer [10000] Window slide size (Any integer
65 value)
66 -cumulative boolean [N] Include to calculate cumulative skew
67 -at boolean [N] Include for observing AT skew instead of
68 GC skew
69 -purine boolean [N] Include for observing purine (AG/TC)
70 skew
71 -keto boolean [N] Include for observing keto (TG/AC) skew
72 -plot toggle [N] Include to plot result
73
74 Associated qualifiers:
75
76 "-sequence" associated qualifiers
77 -sbegin1 integer Start of each sequence to be used
78 -send1 integer End of each sequence to be used
79 -sreverse1 boolean Reverse (if DNA)
80 -sask1 boolean Ask for begin/end/reverse
81 -snucleotide1 boolean Sequence is nucleotide
82 -sprotein1 boolean Sequence is protein
83 -slower1 boolean Make lower case
84 -supper1 boolean Make upper case
85 -scircular1 boolean Sequence is circular
86 -sformat1 string Input sequence format
87 -iquery1 string Input query fields or ID list
88 -ioffset1 integer Input start position offset
89 -sdbname1 string Database name
90 -sid1 string Entryname
91 -ufo1 string UFO features
92 -fformat1 string Features format
93 -fopenfile1 string Features file name
94
95 "-graph" associated qualifiers
96 -gprompt boolean Graph prompting
97 -gdesc string Graph description
98 -gtitle string Graph title
99 -gsubtitle string Graph subtitle
100 -gxtitle string Graph x axis title
101 -gytitle string Graph y axis title
102 -goutfile string Output file for non interactive displays
103 -gdirectory string Output directory
104
105 "-outfile" associated qualifiers
106 -odirectory string Output directory
107
108 General qualifiers:
109 -auto boolean Turn off prompts
110 -stdout boolean Write first file to standard output
111 -filter boolean Read first file from standard input, write
112 first file to standard output
113 -options boolean Prompt for standard and additional values
114 -debug boolean Write debug output to program.dbg
115 -verbose boolean Report some/full command line options
116 -help boolean Report command line options and exit. More
117 information on associated and general
118 qualifiers can be found with -help -verbose
119 -warning boolean Report warnings
120 -error boolean Report errors
121 -fatal boolean Report fatal errors
122 -die boolean Report dying program messages
123 -version boolean Report version number and exit
124
125 Input file format
126
127 The database definitions for following commands are available at
128 http://soap.g-language.org/kbws/embossrc
129
130 ggcskew reads one or more nucleotide sequences.
131
132 Output file format
133
134 The output from ggcskew is to a plain text file or the EMBOSS graphics
135 device.
136
137 File: nc_000913.ggcskew
138
139 Sequence: NC_000913
140 location,GC skew
141 0,-0.035529
142 10000,-0.039648
143 20000,-0.049791
144 30000,0.005072
145 40000,-0.063483
146 50000,-0.030256
147 60000,0.011875
148 70000,-0.029478
149
150 [Part of this file has been deleted for brevity]
151
152 4530000,-0.017164
153 4540000,-0.036140
154 4550000,-0.028166
155 4560000,0.012166
156 4570000,-0.040486
157 4580000,-0.020692
158 4590000,-0.043920
159 4600000,-0.026363
160 4610000,-0.022778
161 4620000,-0.049396
162
163
164 Data files
165
166 None.
167
168 Notes
169
170 None.
171
172 References
173
174 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
175 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
176 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
177
178 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
179 large-scale analysis of high-throughput omics data, J. Pest Sci.,
180 31, 7.
181
182 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
183 Analysis Environment with REST and SOAP Web Service Interfaces,
184 Nucleic Acids Res., 38, W700-W705.
185
186 Warnings
187
188 None.
189
190 Diagnostic Error Messages
191
192 None.
193
194 Exit status
195
196 It always exits with a status of 0.
197
198 Known bugs
199
200 None.
201
202 See also
203
204 ggcwin Calculates the GC content along the given genome
205 ggeneskew Calculate the gene strand bias of the given genome
206 ggenomicskew Calculates the GC skew in different regions of the given genom
207
208 Author(s)
209
210 Hidetoshi Itaya (celery@g-language.org)
211 Institute for Advanced Biosciences, Keio University
212 252-0882 Japan
213
214 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
215 Institute for Advanced Biosciences, Keio University
216 252-0882 Japan
217
218 History
219
220 2012 - Written by Hidetoshi Itaya
221 2013 - Fixed by Hidetoshi Itaya
222
223 Target users
224
225 This program is intended to be used by everyone and everything, from
226 naive users to embedded scripts.
227
228 Comments
229
230 None.
231