Mercurial > repos > ktnyt > gembassy

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Initial upload
author ktnyt
date Fri, 26 Jun 2015 05:19:29 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:8300eb051bea
1 gcircularmap
2 Function
3
4 Draws circular map of the genome
5
6 Description
7
8 gdnawalk creates a circular map of the genome using SVG, suitable for
9 plasmids and circular bacterial chromosomes.
10
11 From the outer ring inwards, genes on direct strand (pink),
12 genes on complementary strand (yellow), tRNAs (green arrows),
13 rRNAs (pink or orange stripes depending on the strand),
14 GC content (brown lines), GC skew (yellow lines). Replication
15 origin and terminus predicted from the GC skew shift points
16 are also labeled.
17
18 G-language SOAP service is provided by the
19 Institute for Advanced Biosciences, Keio University.
20 The original web service is located at the following URL:
21
22 http://www.g-language.org/wiki/soap
23
24 WSDL(RPC/Encoded) file is located at:
25
26 http://soap.g-language.org/g-language.wsdl
27
28 Documentation on G-language Genome Analysis Environment methods are
29 provided at the Document Center
30
31 http://ws.g-language.org/gdoc/
32
33 Usage
34
35 Here is a sample session with gcircularmap
36
37 % gcircularmap refseqn:NC_000913
38 Draws circular map of the genome
39 Created gcircularmap.1.svg
40
41 Go to the input files for this example
42 Go to the output files for this example
43
44 Command line arguments
45
46 Standard (Mandatory) qualifiers:
47 [-sequence] seqall Nucleotide sequence(s) filename and optional
48 format, or reference (input USA)
49
50 Additional (Optional) qualifiers: (none)
51 Advanced (Unprompted) qualifiers:
52 -format string [svg] Output file format. Dependent on
53 'convert' command (Any string)
54 -[no]accid boolean [Y] Include to use sequence accession ID as
55 query
56 -goutfile string [gcircularmap] Output file for non
57 interactive displays (Any string)
58
59 Associated qualifiers:
60
61 "-sequence" associated qualifiers
62 -sbegin1 integer Start of each sequence to be used
63 -send1 integer End of each sequence to be used
64 -sreverse1 boolean Reverse (if DNA)
65 -sask1 boolean Ask for begin/end/reverse
66 -snucleotide1 boolean Sequence is nucleotide
67 -sprotein1 boolean Sequence is protein
68 -slower1 boolean Make lower case
69 -supper1 boolean Make upper case
70 -scircular1 boolean Sequence is circular
71 -sformat1 string Input sequence format
72 -iquery1 string Input query fields or ID list
73 -ioffset1 integer Input start position offset
74 -sdbname1 string Database name
75 -sid1 string Entryname
76 -ufo1 string UFO features
77 -fformat1 string Features format
78 -fopenfile1 string Features file name
79
80 General qualifiers:
81 -auto boolean Turn off prompts
82 -stdout boolean Write first file to standard output
83 -filter boolean Read first file from standard input, write
84 first file to standard output
85 -options boolean Prompt for standard and additional values
86 -debug boolean Write debug output to program.dbg
87 -verbose boolean Report some/full command line options
88 -help boolean Report command line options and exit. More
89 information on associated and general
90 qualifiers can be found with -help -verbose
91 -warning boolean Report warnings
92 -error boolean Report errors
93 -fatal boolean Report fatal errors
94 -die boolean Report dying program messages
95 -version boolean Report version number and exit
96
97 Input file format
98
99 The database definitions for following commands are available at
100 http://soap.g-language.org/kbws/embossrc
101
102 gcircularmap reads one or more nucleotide sequences.
103
104 Output file format
105
106 The output from gcircularmap is to an image file.
107
108 Data files
109
110 None.
111
112 Notes
113
114 None.
115
116 References
117
118 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
119 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
120 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
121
122 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
123 large-scale analysis of high-throughput omics data, J. Pest Sci.,
124 31, 7.
125
126 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
127 Analysis Environment with REST and SOAP Web Service Interfaces,
128 Nucleic Acids Res., 38, W700-W705.
129
130 Warnings
131
132 None.
133
134 Diagnostic Error Messages
135
136 None.
137
138 Exit status
139
140 It always exits with a status of 0.
141
142 Known bugs
143
144 None.
145
146 See also
147
148 gdnawalk Draws DNA Walk map of the genome
149 ggenomemap3 Draws the map of the genome (version 3)
150
151 Author(s)
152
153 Hidetoshi Itaya (celery@g-language.org)
154 Institute for Advanced Biosciences, Keio University
155 252-0882 Japan
156
157 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
158 Institute for Advanced Biosciences, Keio University
159 252-0882 Japan
160
161 History
162
163 2012 - Written by Hidetoshi Itaya
164 2013 - Fixed by Hidetoshi Itaya
165
166 Target users
167
168 This program is intended to be used by everyone and everything, from
169 naive users to embedded scripts.
170
171 Comments
172
173 None.
174