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

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1 gdistincc
2 Function
3
4 Calculates the distance between two loci in circular chromosomes
5
6 Description
7
8 gdistincc calculates the distance between two loci in circular
9 chromosomes. It is mostly useful to calculate the distance from the
10 replication origin.
11
12 G-language SOAP service is provided by the
13 Institute for Advanced Biosciences, Keio University.
14 The original web service is located at the following URL:
15
16 http://www.g-language.org/wiki/soap
17
18 WSDL(RPC/Encoded) file is located at:
19
20 http://soap.g-language.org/g-language.wsdl
21
22 Documentation on G-language Genome Analysis Environment methods are
23 provided at the Document Center
24
25 http://ws.g-language.org/gdoc/
26
27 Usage
28
29 Here is a sample session with gdistincc
30
31 % gdistincc refseqn:NC_000913 1234
32 Calculates the distance between two loci in circular chromosomes
33 Output file [nc_000913.gdistincc]:
34
35 Go to the input files for this example
36 Go to the output files for this example
37
38 Command line arguments
39
40 Standard (Mandatory) qualifiers:
41 [-sequence] seqall Nucleotide sequence(s) filename and optional
42 format, or reference (input USA)
43 [-first] integer [0] Position to find the distance (Any
44 integer value)
45 [-outfile] outfile [*.gdistincc] Output file name
46
47 Additional (Optional) qualifiers: (none)
48 Advanced (Unprompted) qualifiers:
49 -second integer [-1] If the second position is negative,
50 position of replication origin is used (Any
51 integer value)
52 -[no]accid boolean [Y] Include to use sequence accession ID as
53 query
54
55 Associated qualifiers:
56
57 "-sequence" associated qualifiers
58 -sbegin1 integer Start of each sequence to be used
59 -send1 integer End of each sequence to be used
60 -sreverse1 boolean Reverse (if DNA)
61 -sask1 boolean Ask for begin/end/reverse
62 -snucleotide1 boolean Sequence is nucleotide
63 -sprotein1 boolean Sequence is protein
64 -slower1 boolean Make lower case
65 -supper1 boolean Make upper case
66 -scircular1 boolean Sequence is circular
67 -sformat1 string Input sequence format
68 -iquery1 string Input query fields or ID list
69 -ioffset1 integer Input start position offset
70 -sdbname1 string Database name
71 -sid1 string Entryname
72 -ufo1 string UFO features
73 -fformat1 string Features format
74 -fopenfile1 string Features file name
75
76 "-outfile" associated qualifiers
77 -odirectory3 string Output directory
78
79 General qualifiers:
80 -auto boolean Turn off prompts
81 -stdout boolean Write first file to standard output
82 -filter boolean Read first file from standard input, write
83 first file to standard output
84 -options boolean Prompt for standard and additional values
85 -debug boolean Write debug output to program.dbg
86 -verbose boolean Report some/full command line options
87 -help boolean Report command line options and exit. More
88 information on associated and general
89 qualifiers can be found with -help -verbose
90 -warning boolean Report warnings
91 -error boolean Report errors
92 -fatal boolean Report fatal errors
93 -die boolean Report dying program messages
94 -version boolean Report version number and exit
95
96 Input file format
97
98 The database definitions for following commands are available at
99 http://soap.g-language.org/kbws/embossrc
100
101 gdistincc reads one or more nucleotide sequences.
102
103 Output file format
104
105 The output from gdistincc is to a plain text file.
106
107 File: nc_000913.gdistincc
108
109 Sequence: NC_000913 Position1: 1234 Distance 1169193600
110
111
112 Data files
113
114 None.
115
116 Notes
117
118 None.
119
120 References
121
122 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
123 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
124 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
125
126 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
127 large-scale analysis of high-throughput omics data, J. Pest Sci.,
128 31, 7.
129
130 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
131 Analysis Environment with REST and SOAP Web Service Interfaces,
132 Nucleic Acids Res., 38, W700-W705.
133
134 Warnings
135
136 None.
137
138 Diagnostic Error Messages
139
140 None.
141
142 Exit status
143
144 It always exits with a status of 0.
145
146 Known bugs
147
148 None.
149
150 See also
151
152 gconsensus_z Calculate consensus in given array of sequences
153 gpalindrome Searches palindrome sequences
154 gseqinfo Prints out basic nucleotide sequence statistics
155
156 Author(s)
157
158 Hidetoshi Itaya (celery@g-language.org)
159 Institute for Advanced Biosciences, Keio University
160 252-0882 Japan
161
162 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
163 Institute for Advanced Biosciences, Keio University
164 252-0882 Japan
165
166 History
167
168 2012 - Written by Hidetoshi Itaya
169 2013 - Fixed by Hidetoshi Itaya
170
171 Target users
172
173 This program is intended to be used by everyone and everything, from
174 naive users to embedded scripts.
175
176 Comments
177
178 None.
179