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

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1 ggenomicskew
2 Function
3
4 Calculates the GC skew in different regions of the given genome
5
6 Description
7
8 ggenomicskew calculates and plots the GC skew for the whole genome, coding
9 regions, intergenic regions, and the third codon. This program is useful in
10 visualizing various base composition bias within the genome. AT skew can be
11 calculated instead of GC skew by toggling the -at qualifier.
12
13 G-language SOAP service is provided by the
14 Institute for Advanced Biosciences, Keio University.
15 The original web service is located at the following URL:
16
17 http://www.g-language.org/wiki/soap
18
19 WSDL(RPC/Encoded) file is located at:
20
21 http://soap.g-language.org/g-language.wsdl
22
23 Documentation on G-language Genome Analysis Environment methods are
24 provided at the Document Center
25
26 http://ws.g-language.org/gdoc/
27
28 Usage
29
30 Here is a sample session with ggenomicskew
31
32 % ggenomicskew refseqn:NC_000913
33 Calculates the GC skew in different regions of the given genome
34 Program compseq output file (optional) [nc_000913.ggenomicskew]:
35
36 Go to the input files for this example
37 Go to the output files for this example
38
39 Example 2
40
41 % ggenomicskew refseqn:NC_000913 -plot -graph png
42 Calculates the GC skew in different regions of the given genome
43 Created ggenomicskew.1.png
44
45 Go to the input files for this example
46 Go to the output files for this example
47
48 Command line arguments
49
50 Standard (Mandatory) qualifiers (* if not always prompted):
51 [-sequence] seqall Nucleotide sequence(s) filename and optional
52 format, or reference (input USA)
53 * -graph xygraph [$EMBOSS_GRAPHICS value, or x11] Graph type
54 (ps, hpgl, hp7470, hp7580, meta, cps, x11,
55 tek, tekt, none, data, xterm, png, gif, svg)
56 * -outfile outfile [*.ggenomicskew] Program compseq output file
57 (optional)
58
59 Additional (Optional) qualifiers: (none)
60 Advanced (Unprompted) qualifiers:
61 -divide integer [250] Window to divide into (Any integer
62 value)
63 -at boolean [N] Input 1 when observing AT skew instead
64 of GC skew
65 -[no]accid boolean [Y] Include to use sequence accession ID as
66 query
67 -plot toggle [N] Include to plot result
68
69 Associated qualifiers:
70
71 "-sequence" associated qualifiers
72 -sbegin1 integer Start of each sequence to be used
73 -send1 integer End of each sequence to be used
74 -sreverse1 boolean Reverse (if DNA)
75 -sask1 boolean Ask for begin/end/reverse
76 -snucleotide1 boolean Sequence is nucleotide
77 -sprotein1 boolean Sequence is protein
78 -slower1 boolean Make lower case
79 -supper1 boolean Make upper case
80 -scircular1 boolean Sequence is circular
81 -sformat1 string Input sequence format
82 -iquery1 string Input query fields or ID list
83 -ioffset1 integer Input start position offset
84 -sdbname1 string Database name
85 -sid1 string Entryname
86 -ufo1 string UFO features
87 -fformat1 string Features format
88 -fopenfile1 string Features file name
89
90 "-graph" associated qualifiers
91 -gprompt boolean Graph prompting
92 -gdesc string Graph description
93 -gtitle string Graph title
94 -gsubtitle string Graph subtitle
95 -gxtitle string Graph x axis title
96 -gytitle string Graph y axis title
97 -goutfile string Output file for non interactive displays
98 -gdirectory string Output directory
99
100 "-outfile" associated qualifiers
101 -odirectory string Output directory
102
103 General qualifiers:
104 -auto boolean Turn off prompts
105 -stdout boolean Write first file to standard output
106 -filter boolean Read first file from standard input, write
107 first file to standard output
108 -options boolean Prompt for standard and additional values
109 -debug boolean Write debug output to program.dbg
110 -verbose boolean Report some/full command line options
111 -help boolean Report command line options and exit. More
112 information on associated and general
113 qualifiers can be found with -help -verbose
114 -warning boolean Report warnings
115 -error boolean Report errors
116 -fatal boolean Report fatal errors
117 -die boolean Report dying program messages
118 -version boolean Report version number and exit
119
120 Input file format
121
122 The database definitions for following commands are available at
123 http://soap.g-language.org/kbws/embossrc
124
125 ggenomicskew reads one or more nucleotide sequences.
126
127 Output file format
128
129 The output from ggenomicskew is to a plain text file or the EMBOSS graphics device.
130
131 File: nc_000913.ggenomicskew
132
133 Sequence: NC_000913
134 location,GC skew,coding,intergenic,third codon
135 0,-0.036259,-0.040085,-0.034707,-0.141888,
136 1,-0.031167,-0.035657,0.047953,-0.175758,
137 2,-0.028670,-0.031139,-0.049143,-0.018466,
138 3,-0.016647,-0.004656,-0.102616,0.086181,
139 4,-0.041985,-0.029846,-0.088670,0.015291,
140 5,-0.097093,-0.103813,-0.067275,-0.247401,
141 6,-0.028028,-0.016363,-0.048806,-0.047332,
142 7,-0.055805,-0.059329,-0.020071,-0.123271,
143
144 [Part of this file has been deleted for brevity]
145
146 241,0.000772,-0.012151,-0.063786,0.069585,
147 242,-0.025787,-0.000384,-0.049143,0.029431,
148 243,0.010516,0.008217,-0.030600,0.128657,
149 244,-0.037115,-0.015134,0.017500,0.035398,
150 245,-0.000317,0.006021,-0.047170,0.091549,
151 246,-0.025417,-0.015190,-0.116608,0.044619,
152 247,-0.038404,-0.035676,-0.135714,0.015375,
153 248,-0.026246,-0.024240,-0.037190,-0.130118,
154 249,-0.053371,-0.057225,-0.022472,-0.082167,
155 250,-0.026316,0.166667,-0.151515,0.000000,
156
157
158 Data files
159
160 None.
161
162 Notes
163
164 None.
165
166 References
167
168 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
169 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
170 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
171
172 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
173 large-scale analysis of high-throughput omics data, J. Pest Sci.,
174 31, 7.
175
176 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
177 Analysis Environment with REST and SOAP Web Service Interfaces,
178 Nucleic Acids Res., 38, W700-W705.
179
180 Warnings
181
182 None.
183
184 Diagnostic Error Messages
185
186 None.
187
188 Exit status
189
190 It always exits with a status of 0.
191
192 Known bugs
193
194 None.
195
196 See also
197
198 ggcskew Calculates the GC skew of the input sequence
199 ggcwin Calculates the GC content along the given genome
200 ggeneskew Calculate the gene strand bias of the given genome
201
202 Author(s)
203
204 Hidetoshi Itaya (celery@g-language.org)
205 Institute for Advanced Biosciences, Keio University
206 252-0882 Japan
207
208 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
209 Institute for Advanced Biosciences, Keio University
210 252-0882 Japan
211
212 History
213
214 2012 - Written by Hidetoshi Itaya
215 2013 - Fixed by Hidetoshi Itaya
216
217 Target users
218
219 This program is intended to be used by everyone and everything, from
220 naive users to embedded scripts.
221
222 Comments
223
224 None.
225