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

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1 gcgr
2 Function
3
4 Create a Chaos Game Representation of a given sequence
5
6 Description
7
8 gcgr creates a Chaos Game Representation (CGR) image of a given sequence.
9 CGR is generated by the following procedure:
10
11 1. Start from position (0,0) or the origin of two dimensional coordinate.
12 Four nucleotides are located at the four corners:
13 A: (-1, 1) upper left
14 T: (1, -1) lower right
15 G: (1, 1) upper right
16 C: (-1, -1) lower left
17 2. For each nucleotide, move and mark the new location which is halfway
18 between the current location and the nucleotide.
19 For example, if the first letter is A, position is moved from (0,0) to
20 midpoint between (-1, 1) and (0,0), which is (-0.5, 0.5).
21
22 3. Repeat this procedure for all nucleotides.
23 CGR is a generalized scale-independent Markov probability table for the
24 sequence, and oligomer tables can be deduced from CGR image.
25
26 G-language SOAP service is provided by the
27 Institute for Advanced Biosciences, Keio University.
28 The original web service is located at the following URL:
29
30 http://www.g-language.org/wiki/soap
31
32 WSDL(RPC/Encoded) file is located at:
33
34 http://soap.g-language.org/g-language.wsdl
35
36 Documentation on G-language Genome Analysis Environment methods are
37 provided at the Document Center
38
39 http://ws.g-language.org/gdoc/
40
41 Usage
42
43 Here is a sample session with gcgr
44
45 % gcgr refseqn:NC_000913
46 Create a Chaos Game Representation of a given sequence
47 Created gcgr.1.png
48
49 Go to the input files for this example
50 Go to the output files for this example
51
52 Command line arguments
53
54 Standard (Mandatory) qualifiers:
55 [-sequence] seqall Nucleotide sequence(s) filename and optional
56 format, or reference (input USA)
57
58 Additional (Optional) qualifiers: (none)
59 Advanced (Unprompted) qualifiers:
60 -format string [png] Output file format. Dependent on
61 'convert' command (Any string)
62 -width integer [1024] Width of image (Any integer value)
63 -goutfile string [gcgr] Output file for non interactive
64 displays (Any string)
65
66 Associated qualifiers:
67
68 "-sequence" associated qualifiers
69 -sbegin1 integer Start of each sequence to be used
70 -send1 integer End of each sequence to be used
71 -sreverse1 boolean Reverse (if DNA)
72 -sask1 boolean Ask for begin/end/reverse
73 -snucleotide1 boolean Sequence is nucleotide
74 -sprotein1 boolean Sequence is protein
75 -slower1 boolean Make lower case
76 -supper1 boolean Make upper case
77 -scircular1 boolean Sequence is circular
78 -sformat1 string Input sequence format
79 -iquery1 string Input query fields or ID list
80 -ioffset1 integer Input start position offset
81 -sdbname1 string Database name
82 -sid1 string Entryname
83 -ufo1 string UFO features
84 -fformat1 string Features format
85 -fopenfile1 string Features file name
86
87 General qualifiers:
88 -auto boolean Turn off prompts
89 -stdout boolean Write first file to standard output
90 -filter boolean Read first file from standard input, write
91 first file to standard output
92 -options boolean Prompt for standard and additional values
93 -debug boolean Write debug output to program.dbg
94 -verbose boolean Report some/full command line options
95 -help boolean Report command line options and exit. More
96 information on associated and general
97 qualifiers can be found with -help -verbose
98 -warning boolean Report warnings
99 -error boolean Report errors
100 -fatal boolean Report fatal errors
101 -die boolean Report dying program messages
102 -version boolean Report version number and exit
103
104 Input file format
105
106 The database definitions for following commands are available at
107 http://soap.g-language.org/kbws/embossrc
108
109 gcgr reads one or more nucleotide sequences.
110
111 Output file format
112
113 The output from gcgr is to an image file.
114
115 Data files
116
117 None.
118
119 Notes
120
121 None.
122
123 References
124
125 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
126 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
127 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
128
129 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
130 large-scale analysis of high-throughput omics data, J. Pest Sci.,
131 31, 7.
132
133 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
134 Analysis Environment with REST and SOAP Web Service Interfaces,
135 Nucleic Acids Res., 38, W700-W705.
136
137 Warnings
138
139 None.
140
141 Diagnostic Error Messages
142
143 None.
144
145 Exit status
146
147 It always exits with a status of 0.
148
149 Known bugs
150
151 None.
152
153 See also
154
155 gseq2png Converts a sequence to PNG image
156
157 Author(s)
158
159 Hidetoshi Itaya (celery@g-language.org)
160 Institute for Advanced Biosciences, Keio University
161 252-0882 Japan
162
163 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
164 Institute for Advanced Biosciences, Keio University
165 252-0882 Japan
166
167 History
168
169 2012 - Written by Hidetoshi Itaya
170 2013 - Fixed by Hidetoshi Itaya
171
172 Target users
173
174 This program is intended to be used by everyone and everything, from
175 naive users to embedded scripts.
176
177 Comments
178
179 None.
180