annotate GEMBASSY-1.0.3/doc/text/gcgr.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 gcgr
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 Create a Chaos Game Representation of a given sequence
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 gcgr creates a Chaos Game Representation (CGR) image of a given sequence.
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
9 CGR is generated by the following procedure:
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
10
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
11 1. Start from position (0,0) or the origin of two dimensional coordinate.
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
12 Four nucleotides are located at the four corners:
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
13 A: (-1, 1) upper left
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
14 T: (1, -1) lower right
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
15 G: (1, 1) upper right
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
16 C: (-1, -1) lower left
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
17 2. For each nucleotide, move and mark the new location which is halfway
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
18 between the current location and the nucleotide.
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
19 For example, if the first letter is A, position is moved from (0,0) to
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
20 midpoint between (-1, 1) and (0,0), which is (-0.5, 0.5).
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
21
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
22 3. Repeat this procedure for all nucleotides.
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
23 CGR is a generalized scale-independent Markov probability table for the
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
24 sequence, and oligomer tables can be deduced from CGR image.
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
25
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
26 G-language SOAP service is provided by the
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
27 Institute for Advanced Biosciences, Keio University.
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
28 The original web service is located at the following URL:
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
29
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
30 http://www.g-language.org/wiki/soap
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
31
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
32 WSDL(RPC/Encoded) file is located at:
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
33
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
34 http://soap.g-language.org/g-language.wsdl
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
35
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
36 Documentation on G-language Genome Analysis Environment methods are
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
37 provided at the Document Center
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
38
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
39 http://ws.g-language.org/gdoc/
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
40
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
41 Usage
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
42
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
43 Here is a sample session with gcgr
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
44
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
45 % gcgr refseqn:NC_000913
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
46 Create a Chaos Game Representation of a given sequence
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
47 Created gcgr.1.png
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
48
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
49 Go to the input files for this example
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
50 Go to the output files for this example
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
51
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
52 Command line arguments
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
53
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
54 Standard (Mandatory) qualifiers:
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
55 [-sequence] seqall Nucleotide sequence(s) filename and optional
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
56 format, or reference (input USA)
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
57
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
58 Additional (Optional) qualifiers: (none)
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
59 Advanced (Unprompted) qualifiers:
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
60 -format string [png] Output file format. Dependent on
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
61 'convert' command (Any string)
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
62 -width integer [1024] Width of image (Any integer value)
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
63 -goutfile string [gcgr] Output file for non interactive
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
64 displays (Any string)
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
65
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
66 Associated qualifiers:
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
67
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
68 "-sequence" associated qualifiers
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
69 -sbegin1 integer Start of each sequence to be used
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
70 -send1 integer End of each sequence to be used
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
71 -sreverse1 boolean Reverse (if DNA)
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
72 -sask1 boolean Ask for begin/end/reverse
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
73 -snucleotide1 boolean Sequence is nucleotide
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
74 -sprotein1 boolean Sequence is protein
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
75 -slower1 boolean Make lower case
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
76 -supper1 boolean Make upper case
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
77 -scircular1 boolean Sequence is circular
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
78 -sformat1 string Input sequence format
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
79 -iquery1 string Input query fields or ID list
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
80 -ioffset1 integer Input start position offset
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
81 -sdbname1 string Database name
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
82 -sid1 string Entryname
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
83 -ufo1 string UFO features
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
84 -fformat1 string Features format
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
85 -fopenfile1 string Features file name
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
86
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
87 General qualifiers:
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
88 -auto boolean Turn off prompts
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
89 -stdout boolean Write first file to standard output
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
90 -filter boolean Read first file from standard input, write
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
91 first file to standard output
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
92 -options boolean Prompt for standard and additional values
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
93 -debug boolean Write debug output to program.dbg
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
94 -verbose boolean Report some/full command line options
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
95 -help boolean Report command line options and exit. More
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
96 information on associated and general
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
97 qualifiers can be found with -help -verbose
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
98 -warning boolean Report warnings
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
99 -error boolean Report errors
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
100 -fatal boolean Report fatal errors
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
101 -die boolean Report dying program messages
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
102 -version boolean Report version number and exit
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
103
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
104 Input file format
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
105
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
106 The database definitions for following commands are available at
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
107 http://soap.g-language.org/kbws/embossrc
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
108
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
109 gcgr reads one or more nucleotide sequences.
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
110
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
111 Output file format
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
112
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
113 The output from gcgr is to an image file.
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
114
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
115 Data files
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
116
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
117 None.
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
118
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
119 Notes
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
120
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
121 None.
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
122
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
123 References
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
124
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
125 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
126 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
127 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
128
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
129 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
130 large-scale analysis of high-throughput omics data, J. Pest Sci.,
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
131 31, 7.
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
132
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
133 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
134 Analysis Environment with REST and SOAP Web Service Interfaces,
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
135 Nucleic Acids Res., 38, W700-W705.
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
136
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
137 Warnings
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
138
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
139 None.
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
140
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
141 Diagnostic Error Messages
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
142
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
143 None.
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
144
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
145 Exit status
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
146
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
147 It always exits with a status of 0.
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
148
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
149 Known bugs
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
150
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
151 None.
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
152
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
153 See also
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
154
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
155 gseq2png Converts a sequence to PNG image
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
156
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
157 Author(s)
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
158
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
159 Hidetoshi Itaya (celery@g-language.org)
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
160 Institute for Advanced Biosciences, Keio University
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
161 252-0882 Japan
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
162
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
163 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
164 Institute for Advanced Biosciences, Keio University
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
165 252-0882 Japan
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
166
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
167 History
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
168
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
169 2012 - Written by Hidetoshi Itaya
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
170 2013 - Fixed by Hidetoshi Itaya
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
171
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
172 Target users
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
173
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
174 This program is intended to be used by everyone and everything, from
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
175 naive users to embedded scripts.
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
176
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
177 Comments
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
178
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
179 None.
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
180