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

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1 greporiter
2 Function
3
4 Get the positions of replication origin and terminus
5
6 Description
7
8 greporiter returns the positions of replication origin and terminus
9 in bacterial genomes by several means.
10
11 1. Use of databases
12 By default, grep_ori_ter tries to retrieve the position of replication
13 origin in DoriC Gao and Zhang (2007) database, and the position of
14 replication terminus from the supplemental data provided in
15 Kono et al. (2011).
16 If the position of origin cannot be found in the database, but "rep_origin"
17 feature is available, center position within this feature is used for
18 origin.
19
20 2. Oriloc
21 Using -orilocoption, you can predict the replication origin and
22 terminus using the popular Oriloc program developed by Lobry et al.
23 available as part of the SeqinR package Frank and Lobry (2000).
24
25 3. Use GC skew shift-point
26 If the positions of origin or terminus cannot be found in the databases,
27 grep_ori_ter automatically calls find_ori_ter() method to predict the
28 positions using GC skew shift-points at one-base-pair resolution.
29
30 G-language SOAP service is provided by the
31 Institute for Advanced Biosciences, Keio University.
32 The original web service is located at the following URL:
33
34 http://www.g-language.org/wiki/soap
35
36 WSDL(RPC/Encoded) file is located at:
37
38 http://soap.g-language.org/g-language.wsdl
39
40 Documentation on G-language Genome Analysis Environment methods are
41 provided at the Document Center
42
43 http://ws.g-language.org/gdoc/
44
45 Usage
46
47 Here is a sample session with greporiter
48
49 % greporiter refseqn:NC_000913
50 Get the positions of replication origin and terminus
51 Output file [nc_000913.greporiter]:
52
53 Go to the input files for this example
54 Go to the output files for this example
55
56 Command line arguments
57
58 Standard (Mandatory) qualifiers:
59 [-sequence] seqall Nucleotide sequence(s) filename and optional
60 format, or reference (input USA)
61 [-outfile] outfile [*.greporiter] Output file name
62
63 Additional (Optional) qualifiers: (none)
64 Advanced (Unprompted) qualifiers:
65 -oriloc boolean [N] Include Oriloc for prediction
66 -gcskew boolean [N] Include to use GC skew shift-point for
67 prediction
68 -difthreshold integer [0] Distance between the GC skew shift point
69 and predicted dif site expressed as the
70 precentage of genome size, used as a
71 threshold to retrieve dif sequence from the
72 database (Any integer value)
73 -dbonly boolean [N] Include to only use values available in
74 databases and to suppress prediction
75 -[no]accid boolean [Y] Include to use sequence accession ID as
76 query
77
78 Associated qualifiers:
79
80 "-sequence" associated qualifiers
81 -sbegin1 integer Start of each sequence to be used
82 -send1 integer End of each sequence to be used
83 -sreverse1 boolean Reverse (if DNA)
84 -sask1 boolean Ask for begin/end/reverse
85 -snucleotide1 boolean Sequence is nucleotide
86 -sprotein1 boolean Sequence is protein
87 -slower1 boolean Make lower case
88 -supper1 boolean Make upper case
89 -scircular1 boolean Sequence is circular
90 -sformat1 string Input sequence format
91 -iquery1 string Input query fields or ID list
92 -ioffset1 integer Input start position offset
93 -sdbname1 string Database name
94 -sid1 string Entryname
95 -ufo1 string UFO features
96 -fformat1 string Features format
97 -fopenfile1 string Features file name
98
99 "-outfile" associated qualifiers
100 -odirectory2 string Output directory
101
102 General qualifiers:
103 -auto boolean Turn off prompts
104 -stdout boolean Write first file to standard output
105 -filter boolean Read first file from standard input, write
106 first file to standard output
107 -options boolean Prompt for standard and additional values
108 -debug boolean Write debug output to program.dbg
109 -verbose boolean Report some/full command line options
110 -help boolean Report command line options and exit. More
111 information on associated and general
112 qualifiers can be found with -help -verbose
113 -warning boolean Report warnings
114 -error boolean Report errors
115 -fatal boolean Report fatal errors
116 -die boolean Report dying program messages
117 -version boolean Report version number and exit
118
119 Input file format
120
121 The database definitions for following commands are available at
122 http://soap.g-language.org/kbws/embossrc
123
124 greporiter reads one or more nucleotide sequences.
125
126 Output file format
127
128 The output from greporiter is to a plain text file.
129
130 File: nc_000913.greporiter
131
132 Sequence: NC_000913 Origin: 3923881 Terminus: 1550412
133
134
135 Data files
136
137 None.
138
139 Notes
140
141 None.
142
143 References
144
145 Gao F and Zhang CT (2007) DoriC: a database of oriC regions in bacterial
146 genomes, Bioinformatics, 23(14):1866-1867
147
148 Kono N et al. (2011) Comprehensive prediction of chromosome dimer resolution
149 sites in bacterial genomes, BMC Genomics, 12(1):19
150
151 Frank AC and Lobry JR (2000) "Oriloc: prediction of replication boundaries
152 in unannotated bacterial chromosomes", Bioinformatics, 16(6):560-561
153
154 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
155 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
156 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
157
158 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
159 large-scale analysis of high-throughput omics data, J. Pest Sci.,
160 31, 7.
161
162 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
163 Analysis Environment with REST and SOAP Web Service Interfaces,
164 Nucleic Acids Res., 38, W700-W705.
165
166 Warnings
167
168 None.
169
170 Diagnostic Error Messages
171
172 None.
173
174 Exit status
175
176 It always exits with a status of 0.
177
178 Known bugs
179
180 None.
181
182 See also
183
184 gfindoriter Predicts the replication origin and terminus in bacterial
185 genomes
186
187 Author(s)
188
189 Hidetoshi Itaya (celery@g-language.org)
190 Institute for Advanced Biosciences, Keio University
191 252-0882 Japan
192
193 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
194 Institute for Advanced Biosciences, Keio University
195 252-0882 Japan
196
197 History
198
199 2012 - Written by Hidetoshi Itaya
200 2013 - Fixed by Hidetoshi Itaya
201
202 Target users
203
204 This program is intended to be used by everyone and everything, from
205 naive users to embedded scripts.
206
207 Comments
208
209 None.
210