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

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1 gfindoriter
2 Function
3
4 Predict the replication origin and terminus in bacterial genomes
5
6 Description
7
8 gfindoriter predicts the replicational origin and terminus in circular
9 bacterial genomes, by taking the vertices of cumulative skew graphs (GC,
10 d keto, or purine). See Frank and Lobry (2000) for the basic idea behind
11 this algorithm (but also note that this algorithm is different from that
12 of Oriloc, which uses GC3 of genes).
13 Terminus of replication can be more accurate by using noise-reduction
14 filtering using Fourier spectrum of the GC skew. This low-pass filtering
15 can be applied using -filter option. See Arakawa et al. (2007) for details.
16
17 G-language SOAP service is provided by the
18 Institute for Advanced Biosciences, Keio University.
19 The original web service is located at the following URL:
20
21 http://www.g-language.org/wiki/soap
22
23 WSDL(RPC/Encoded) file is located at:
24
25 http://soap.g-language.org/g-language.wsdl
26
27 Documentation on G-language Genome Analysis Environment methods are
28 provided at the Document Center
29
30 http://ws.g-language.org/gdoc/
31
32 Usage
33
34 Here is a sample session with gfindoriter
35
36 % gfindoriter refseqn:NC_000913
37 Predict the replication origin and terminus in bacterial genomes
38 Output file [nc_000913.gfindoriter]:
39
40 Go to the input files for this example
41 Go to the output files for this example
42
43 Command line arguments
44
45 Standard (Mandatory) qualifiers:
46 [-sequence] seqall Nucleotide sequence(s) filename and optional
47 format, or reference (input USA)
48 [-outfile] outfile [*.gfindoriter] Output file name
49
50 Additional (Optional) qualifiers: (none)
51 Advanced (Unprompted) qualifiers:
52 -window integer [4096] Number of windows to use for Fat
53 Fourier Transform. Only active when -lowpass
54 option is specified. Value must be the
55 power of two (Any integer value)
56 -purine boolean [N] Use purine skew for calculation
57 -keto boolean [N] Use keto skew for calculation
58 -lowpass integer [0] Lowpass filter strength in percent.
59 Typically 95 or 99 works best (Any integer
60 value)
61 -[no]accid boolean [Y] Include to use sequence accession ID as
62 query
63
64 Associated qualifiers:
65
66 "-sequence" associated qualifiers
67 -sbegin1 integer Start of each sequence to be used
68 -send1 integer End of each sequence to be used
69 -sreverse1 boolean Reverse (if DNA)
70 -sask1 boolean Ask for begin/end/reverse
71 -snucleotide1 boolean Sequence is nucleotide
72 -sprotein1 boolean Sequence is protein
73 -slower1 boolean Make lower case
74 -supper1 boolean Make upper case
75 -scircular1 boolean Sequence is circular
76 -sformat1 string Input sequence format
77 -iquery1 string Input query fields or ID list
78 -ioffset1 integer Input start position offset
79 -sdbname1 string Database name
80 -sid1 string Entryname
81 -ufo1 string UFO features
82 -fformat1 string Features format
83 -fopenfile1 string Features file name
84
85 "-outfile" associated qualifiers
86 -odirectory2 string Output directory
87
88 General qualifiers:
89 -auto boolean Turn off prompts
90 -stdout boolean Write first file to standard output
91 -filter boolean Read first file from standard input, write
92 first file to standard output
93 -options boolean Prompt for standard and additional values
94 -debug boolean Write debug output to program.dbg
95 -verbose boolean Report some/full command line options
96 -help boolean Report command line options and exit. More
97 information on associated and general
98 qualifiers can be found with -help -verbose
99 -warning boolean Report warnings
100 -error boolean Report errors
101 -fatal boolean Report fatal errors
102 -die boolean Report dying program messages
103 -version boolean Report version number and exit
104
105 Input file format
106
107 The database definitions for following commands are available at
108 http://soap.g-language.org/kbws/embossrc
109
110 gfindoriter reads one or more nucleotide sequences.
111
112 Output file format
113
114 The output from gfindoriter is to a plain text file.
115
116 File: nc_000913.gfindoriter
117
118 Sequence: NC_000913 Origin: 3922946 Terminus: 1550274
119
120
121 Data files
122
123 None.
124
125 Notes
126
127 None.
128
129 References
130
131 Frank AC, Lobry JR (2000) Oriloc: prediction of replication boundaries in
132 unannotated bacterial chromosomes, Bioinformatics, 16:566-567.
133
134 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
135 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
136 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
137
138 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
139 large-scale analysis of high-throughput omics data, J. Pest Sci.,
140 31, 7.
141
142 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
143 Analysis Environment with REST and SOAP Web Service Interfaces,
144 Nucleic Acids Res., 38, W700-W705.
145
146 Warnings
147
148 None.
149
150 Diagnostic Error Messages
151
152 None.
153
154 Exit status
155
156 It always exits with a status of 0.
157
158 Known bugs
159
160 None.
161
162 See also
163
164 greporiter Gets the positions of replication origin and terminus
165
166 Author(s)
167
168 Hidetoshi Itaya (celery@g-language.org)
169 Institute for Advanced Biosciences, Keio University
170 252-0882 Japan
171
172 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
173 Institute for Advanced Biosciences, Keio University
174 252-0882 Japan
175
176 History
177
178 2012 - Written by Hidetoshi Itaya
179 2013 - Fixed by Hidetoshi Itaya
180
181 Target users
182
183 This program is intended to be used by everyone and everything, from
184 naive users to embedded scripts.
185
186 Comments
187
188 None.
189