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comparison GEMBASSY-1.0.3/doc/text/gb2.txt @ 0:8300eb051bea draft

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1 gb2
2 Function
3
4 Calculate strand bias of bacterial genome using B2 index
5
6 Description
7
8 gb2 calculates strand bias of bacterial genome using B2 index,
9 proposed by Lobry and Sueoka(2002). Basic idea of B2 index is to calculate
10 the distance from neutral parity state (0.5, 0.5), when the bias of
11 the coding regions is plotted in a coordinate system with axes representing
12 G/(G+C) and A/(A+T), using the third codon position of genes. This index
13 measures the degree of transcription- and translation-associated effects of
14 bias from Chargaff's second parity rule.
15
16 G-language SOAP service is provided by the
17 Institute for Advanced Biosciences, Keio University.
18 The original web service is located at the following URL:
19
20 http://www.g-language.org/wiki/soap
21
22 WSDL(RPC/Encoded) file is located at:
23
24 http://soap.g-language.org/g-language.wsdl
25
26 Documentation on G-language Genome Analysis Environment methods are
27 provided at the Document Center
28
29 http://ws.g-language.org/gdoc/
30
31 Usage
32
33 Here is a sample session with gb2
34
35 % gb2 refseqn:NC_000913
36 Calculate strand bias of bacterial genome using B2 index
37 Program compseq output file [nc_000913.gb2]:
38
39 Go to the input files for this example
40 Go to the output files for this example
41
42 Command line arguments
43
44 Standard (Mandatory) qualifiers:
45 [-sequence] seqall Nucleotide sequence(s) filename and optional
46 format, or reference (input USA)
47 [-outfile] outfile [*.gb2] Program compseq output file
48
49 Additional (Optional) qualifiers: (none)
50 Advanced (Unprompted) qualifiers:
51 -[no]accid boolean [Y] Include to use sequence accession ID as
52 query
53
54 Associated qualifiers:
55
56 "-sequence" associated qualifiers
57 -sbegin1 integer Start of each sequence to be used
58 -send1 integer End of each sequence to be used
59 -sreverse1 boolean Reverse (if DNA)
60 -sask1 boolean Ask for begin/end/reverse
61 -snucleotide1 boolean Sequence is nucleotide
62 -sprotein1 boolean Sequence is protein
63 -slower1 boolean Make lower case
64 -supper1 boolean Make upper case
65 -scircular1 boolean Sequence is circular
66 -sformat1 string Input sequence format
67 -iquery1 string Input query fields or ID list
68 -ioffset1 integer Input start position offset
69 -sdbname1 string Database name
70 -sid1 string Entryname
71 -ufo1 string UFO features
72 -fformat1 string Features format
73 -fopenfile1 string Features file name
74
75 "-outfile" associated qualifiers
76 -odirectory2 string Output directory
77
78 General qualifiers:
79 -auto boolean Turn off prompts
80 -stdout boolean Write first file to standard output
81 -filter boolean Read first file from standard input, write
82 first file to standard output
83 -options boolean Prompt for standard and additional values
84 -debug boolean Write debug output to program.dbg
85 -verbose boolean Report some/full command line options
86 -help boolean Report command line options and exit. More
87 information on associated and general
88 qualifiers can be found with -help -verbose
89 -warning boolean Report warnings
90 -error boolean Report errors
91 -fatal boolean Report fatal errors
92 -die boolean Report dying program messages
93 -version boolean Report version number and exit
94
95 Input file format
96
97 The database definitions for following commands are available at
98 http://soap.g-language.org/kbws/embossrc
99
100 gb2 reads one or more nucleotide sequences.
101
102 Output file format
103
104 The output from gb2 is to a plain text file.
105
106 File: nc_000913.gb2
107
108 Sequence: NC_000913 B2: 0.0919769585775651
109
110
111 Data files
112
113 None.
114
115 Notes
116
117 None.
118
119 References
120
121 Lobry JR and Sueoka N (2002) Asymmetric directional mutation pressures in
122 bacteria, Genome Biology, 3(10):0058
123
124 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
125 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
126 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
127
128 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
129 large-scale analysis of high-throughput omics data, J. Pest Sci.,
130 31, 7.
131
132 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
133 Analysis Environment with REST and SOAP Web Service Interfaces,
134 Nucleic Acids Res., 38, W700-W705.
135
136 Warnings
137
138 None.
139
140 Diagnostic Error Messages
141
142 None.
143
144 Exit status
145
146 It always exits with a status of 0.
147
148 Known bugs
149
150 None.
151
152 See also
153
154 gb1 Calculate strand bias of bacterial genome using B1 index
155 gdeltagcskew Calculate strand bias of bacterial genome using delta GC skew
156 index
157 ggcsi GC Skew Index: an index for strand-specefic mutational bias
158 gldabias Calculate strand bias of bacterial genome using linear
159 discriminant analysis (LDA)
160
161 Author(s)
162
163 Hidetoshi Itaya (celery@g-language.org)
164 Institute for Advanced Biosciences, Keio University
165 252-0882 Japan
166
167 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
168 Institute for Advanced Biosciences, Keio University
169 252-0882 Japan
170
171 History
172
173 2012 - Written by Hidetoshi Itaya
174 2013 - Fixed by Hidetoshi Itaya
175
176 Target users
177
178 This program is intended to be used by everyone and everything, from
179 naive users to embedded scripts.
180
181 Comments
182
183 None.
184