Mercurial > repos > ktnyt > gembassy
comparison GEMBASSY-1.0.3/doc/text/ggeneskew.txt @ 0:8300eb051bea draft
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author | ktnyt |
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date | Fri, 26 Jun 2015 05:19:29 -0400 |
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1 ggeneskew | |
2 Function | |
3 | |
4 Calculate the gene strand bias of the given genome | |
5 | |
6 Description | |
7 | |
8 ggeneskew calculates and plots the strand bias of genes (or the GC skew | |
9 within them). By default, this program visualizes the gene strand preference | |
10 (1 for direct, -1 for complement strand), but by specifying -base option | |
11 option, GC/AT/Purine/Keto skews of the coding regions or more specifically | |
12 in the GC3 (third codon position) with -gctri option can be calculated. | |
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 ggeneskew | |
32 | |
33 % ggeneskew refseqn:NC_000913 | |
34 Calculate the gene strand bias of the given genome | |
35 Program compseq output file (optional) [nc_000913.ggeneskew]: | |
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 % ggeneskew refseqn:NC_000913 -plot -graph png | |
43 Calculate the gene strand bias of the given genome | |
44 Created ggeneskew.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 [*.ggeneskew] 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] Input 1 to calculate cumulative skew | |
67 -base selection [none] Input 'gc', 'at', 'purine', or 'keto' | |
68 for observing GC/AT/Purine/Keto skews | |
69 -gctri boolean [N] Include to use only the third codon | |
70 positions | |
71 -[no]accid boolean [Y] Include to use sequence accession ID as | |
72 query | |
73 -plot toggle [N] Include to plot result | |
74 | |
75 Associated qualifiers: | |
76 | |
77 "-sequence" associated qualifiers | |
78 -sbegin1 integer Start of each sequence to be used | |
79 -send1 integer End of each sequence to be used | |
80 -sreverse1 boolean Reverse (if DNA) | |
81 -sask1 boolean Ask for begin/end/reverse | |
82 -snucleotide1 boolean Sequence is nucleotide | |
83 -sprotein1 boolean Sequence is protein | |
84 -slower1 boolean Make lower case | |
85 -supper1 boolean Make upper case | |
86 -scircular1 boolean Sequence is circular | |
87 -sformat1 string Input sequence format | |
88 -iquery1 string Input query fields or ID list | |
89 -ioffset1 integer Input start position offset | |
90 -sdbname1 string Database name | |
91 -sid1 string Entryname | |
92 -ufo1 string UFO features | |
93 -fformat1 string Features format | |
94 -fopenfile1 string Features file name | |
95 | |
96 "-graph" associated qualifiers | |
97 -gprompt boolean Graph prompting | |
98 -gdesc string Graph description | |
99 -gtitle string Graph title | |
100 -gsubtitle string Graph subtitle | |
101 -gxtitle string Graph x axis title | |
102 -gytitle string Graph y axis title | |
103 -goutfile string Output file for non interactive displays | |
104 -gdirectory string Output directory | |
105 | |
106 "-outfile" associated qualifiers | |
107 -odirectory string Output directory | |
108 | |
109 General qualifiers: | |
110 -auto boolean Turn off prompts | |
111 -stdout boolean Write first file to standard output | |
112 -filter boolean Read first file from standard input, write | |
113 first file to standard output | |
114 -options boolean Prompt for standard and additional values | |
115 -debug boolean Write debug output to program.dbg | |
116 -verbose boolean Report some/full command line options | |
117 -help boolean Report command line options and exit. More | |
118 information on associated and general | |
119 qualifiers can be found with -help -verbose | |
120 -warning boolean Report warnings | |
121 -error boolean Report errors | |
122 -fatal boolean Report fatal errors | |
123 -die boolean Report dying program messages | |
124 -version boolean Report version number and exit | |
125 | |
126 Input file format | |
127 | |
128 The database definitions for following commands are available at | |
129 http://soap.g-language.org/kbws/embossrc | |
130 | |
131 ggeneskew reads one or more nucleotide sequences. | |
132 | |
133 Output file format | |
134 | |
135 The output from ggeneskew is to a plain text file or the EMBOSS graphics | |
136 device. | |
137 | |
138 File: nc_000913.ggeneskew | |
139 | |
140 Sequence: NC_000913 | |
141 location,gene None skew | |
142 190,0.294118 | |
143 337,-0.058914 | |
144 2801,-0.120000 | |
145 3734,-0.070588 | |
146 5234,0.037500 | |
147 5683,0.020725 | |
148 6529,0.032765 | |
149 8238,-0.028226 | |
150 | |
151 [Part of this file has been deleted for brevity] | |
152 | |
153 4631820,-0.093407 | |
154 4632464,-0.006479 | |
155 4633544,-0.120690 | |
156 4634030,-0.060367 | |
157 4634719,-0.104167 | |
158 4636201,-0.144560 | |
159 4637613,0.010929 | |
160 4638425,0.200000 | |
161 4638965,-0.081871 | |
162 , | |
163 | |
164 | |
165 Data files | |
166 | |
167 None. | |
168 | |
169 Notes | |
170 | |
171 None. | |
172 | |
173 References | |
174 | |
175 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and | |
176 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench | |
177 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. | |
178 | |
179 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for | |
180 large-scale analysis of high-throughput omics data, J. Pest Sci., | |
181 31, 7. | |
182 | |
183 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome | |
184 Analysis Environment with REST and SOAP Web Service Interfaces, | |
185 Nucleic Acids Res., 38, W700-W705. | |
186 | |
187 Warnings | |
188 | |
189 None. | |
190 | |
191 Diagnostic Error Messages | |
192 | |
193 None. | |
194 | |
195 Exit status | |
196 | |
197 It always exits with a status of 0. | |
198 | |
199 Known bugs | |
200 | |
201 None. | |
202 | |
203 See also | |
204 | |
205 ggcskew Calculates the GC skew of the input sequence | |
206 ggcwin Calculates the GC content along the given genome | |
207 ggenomicskew Calculates the GC skew in different regions of the given genom | |
208 | |
209 Author(s) | |
210 | |
211 Hidetoshi Itaya (celery@g-language.org) | |
212 Institute for Advanced Biosciences, Keio University | |
213 252-0882 Japan | |
214 | |
215 Kazuharu Arakawa (gaou@sfc.keio.ac.jp) | |
216 Institute for Advanced Biosciences, Keio University | |
217 252-0882 Japan | |
218 | |
219 History | |
220 | |
221 2012 - Written by Hidetoshi Itaya | |
222 2013 - Fixed by Hidetoshi Itaya | |
223 | |
224 Target users | |
225 | |
226 This program is intended to be used by everyone and everything, from | |
227 naive users to embedded scripts. | |
228 | |
229 Comments | |
230 | |
231 None. | |
232 |