annotate GEMBASSY-1.0.3/doc/text/ggenomicskew.txt @ 1:84a17b3fad1f draft

Uploaded
author ktnyt
date Fri, 26 Jun 2015 05:20:29 -0400
parents 8300eb051bea
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
1 ggenomicskew
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
2 Function
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
3
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
4 Calculates the GC skew in different regions of the given genome
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
5
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
6 Description
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
7
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
8 ggenomicskew calculates and plots the GC skew for the whole genome, coding
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
9 regions, intergenic regions, and the third codon. This program is useful in
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
10 visualizing various base composition bias within the genome. AT skew can be
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
11 calculated instead of GC skew by toggling the -at qualifier.
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
12
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
13 G-language SOAP service is provided by the
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
14 Institute for Advanced Biosciences, Keio University.
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
15 The original web service is located at the following URL:
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
16
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
17 http://www.g-language.org/wiki/soap
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
18
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
19 WSDL(RPC/Encoded) file is located at:
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
20
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
21 http://soap.g-language.org/g-language.wsdl
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
22
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
23 Documentation on G-language Genome Analysis Environment methods are
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
24 provided at the Document Center
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
25
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
26 http://ws.g-language.org/gdoc/
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
27
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
28 Usage
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
29
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
30 Here is a sample session with ggenomicskew
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
31
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
32 % ggenomicskew refseqn:NC_000913
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
33 Calculates the GC skew in different regions of the given genome
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
34 Program compseq output file (optional) [nc_000913.ggenomicskew]:
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
35
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
36 Go to the input files for this example
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
37 Go to the output files for this example
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
38
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
39 Example 2
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
40
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
41 % ggenomicskew refseqn:NC_000913 -plot -graph png
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
42 Calculates the GC skew in different regions of the given genome
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
43 Created ggenomicskew.1.png
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
44
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
45 Go to the input files for this example
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
46 Go to the output files for this example
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
47
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
48 Command line arguments
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
49
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
50 Standard (Mandatory) qualifiers (* if not always prompted):
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
51 [-sequence] seqall Nucleotide sequence(s) filename and optional
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
52 format, or reference (input USA)
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
53 * -graph xygraph [$EMBOSS_GRAPHICS value, or x11] Graph type
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
54 (ps, hpgl, hp7470, hp7580, meta, cps, x11,
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
55 tek, tekt, none, data, xterm, png, gif, svg)
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
56 * -outfile outfile [*.ggenomicskew] Program compseq output file
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
57 (optional)
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
58
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
59 Additional (Optional) qualifiers: (none)
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
60 Advanced (Unprompted) qualifiers:
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
61 -divide integer [250] Window to divide into (Any integer
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
62 value)
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
63 -at boolean [N] Input 1 when observing AT skew instead
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
64 of GC skew
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
65 -[no]accid boolean [Y] Include to use sequence accession ID as
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
66 query
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
67 -plot toggle [N] Include to plot result
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
68
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
69 Associated qualifiers:
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
70
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
71 "-sequence" associated qualifiers
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
72 -sbegin1 integer Start of each sequence to be used
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
73 -send1 integer End of each sequence to be used
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
74 -sreverse1 boolean Reverse (if DNA)
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
75 -sask1 boolean Ask for begin/end/reverse
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
76 -snucleotide1 boolean Sequence is nucleotide
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
77 -sprotein1 boolean Sequence is protein
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
78 -slower1 boolean Make lower case
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
79 -supper1 boolean Make upper case
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
80 -scircular1 boolean Sequence is circular
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
81 -sformat1 string Input sequence format
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
82 -iquery1 string Input query fields or ID list
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
83 -ioffset1 integer Input start position offset
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
84 -sdbname1 string Database name
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
85 -sid1 string Entryname
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
86 -ufo1 string UFO features
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
87 -fformat1 string Features format
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
88 -fopenfile1 string Features file name
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
89
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
90 "-graph" associated qualifiers
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
91 -gprompt boolean Graph prompting
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
92 -gdesc string Graph description
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
93 -gtitle string Graph title
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
94 -gsubtitle string Graph subtitle
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
95 -gxtitle string Graph x axis title
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
96 -gytitle string Graph y axis title
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
97 -goutfile string Output file for non interactive displays
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
98 -gdirectory string Output directory
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
99
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
100 "-outfile" associated qualifiers
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
101 -odirectory string Output directory
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
102
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
103 General qualifiers:
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
104 -auto boolean Turn off prompts
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
105 -stdout boolean Write first file to standard output
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
106 -filter boolean Read first file from standard input, write
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
107 first file to standard output
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
108 -options boolean Prompt for standard and additional values
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
109 -debug boolean Write debug output to program.dbg
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
110 -verbose boolean Report some/full command line options
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
111 -help boolean Report command line options and exit. More
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
112 information on associated and general
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
113 qualifiers can be found with -help -verbose
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
114 -warning boolean Report warnings
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
115 -error boolean Report errors
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
116 -fatal boolean Report fatal errors
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
117 -die boolean Report dying program messages
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
118 -version boolean Report version number and exit
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
119
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
120 Input file format
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
121
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
122 The database definitions for following commands are available at
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
123 http://soap.g-language.org/kbws/embossrc
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
124
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
125 ggenomicskew reads one or more nucleotide sequences.
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
126
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
127 Output file format
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
128
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
129 The output from ggenomicskew is to a plain text file or the EMBOSS graphics device.
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
130
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
131 File: nc_000913.ggenomicskew
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
132
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
133 Sequence: NC_000913
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
134 location,GC skew,coding,intergenic,third codon
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
135 0,-0.036259,-0.040085,-0.034707,-0.141888,
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
136 1,-0.031167,-0.035657,0.047953,-0.175758,
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
137 2,-0.028670,-0.031139,-0.049143,-0.018466,
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
138 3,-0.016647,-0.004656,-0.102616,0.086181,
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
139 4,-0.041985,-0.029846,-0.088670,0.015291,
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
140 5,-0.097093,-0.103813,-0.067275,-0.247401,
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
141 6,-0.028028,-0.016363,-0.048806,-0.047332,
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
142 7,-0.055805,-0.059329,-0.020071,-0.123271,
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
143
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
144 [Part of this file has been deleted for brevity]
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
145
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
146 241,0.000772,-0.012151,-0.063786,0.069585,
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
147 242,-0.025787,-0.000384,-0.049143,0.029431,
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
148 243,0.010516,0.008217,-0.030600,0.128657,
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
149 244,-0.037115,-0.015134,0.017500,0.035398,
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
150 245,-0.000317,0.006021,-0.047170,0.091549,
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
151 246,-0.025417,-0.015190,-0.116608,0.044619,
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
152 247,-0.038404,-0.035676,-0.135714,0.015375,
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
153 248,-0.026246,-0.024240,-0.037190,-0.130118,
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
154 249,-0.053371,-0.057225,-0.022472,-0.082167,
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
155 250,-0.026316,0.166667,-0.151515,0.000000,
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
156
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
157
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
158 Data files
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
159
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
160 None.
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
161
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
162 Notes
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
163
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
164 None.
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
165
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
166 References
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
167
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
168 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
169 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
170 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
171
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
172 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
173 large-scale analysis of high-throughput omics data, J. Pest Sci.,
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
174 31, 7.
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
175
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
176 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
177 Analysis Environment with REST and SOAP Web Service Interfaces,
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
178 Nucleic Acids Res., 38, W700-W705.
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
179
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
180 Warnings
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
181
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
182 None.
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
183
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
184 Diagnostic Error Messages
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
185
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
186 None.
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
187
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
188 Exit status
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
189
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
190 It always exits with a status of 0.
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
191
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
192 Known bugs
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
193
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
194 None.
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
195
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
196 See also
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
197
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
198 ggcskew Calculates the GC skew of the input sequence
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
199 ggcwin Calculates the GC content along the given genome
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
200 ggeneskew Calculate the gene strand bias of the given genome
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
201
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
202 Author(s)
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
203
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
204 Hidetoshi Itaya (celery@g-language.org)
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
205 Institute for Advanced Biosciences, Keio University
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
206 252-0882 Japan
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
207
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
208 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
209 Institute for Advanced Biosciences, Keio University
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
210 252-0882 Japan
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
211
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
212 History
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
213
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
214 2012 - Written by Hidetoshi Itaya
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
215 2013 - Fixed by Hidetoshi Itaya
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
216
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
217 Target users
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
218
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
219 This program is intended to be used by everyone and everything, from
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
220 naive users to embedded scripts.
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
221
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
222 Comments
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
223
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
224 None.
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
225