|
0
|
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
|
