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comparison GEMBASSY-1.0.3/doc/text/gb1.txt @ 0:8300eb051bea draft

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1 gb1
2 Function
3
4 Calculate strand bias of bacterial genome using B1 index
5
6 Description
7
8 gb1 calculates the strand bias of bacterial genome using B1 index,
9 first proposed by Lobry and Sueoka (2002), and further extended by
10 Rocha et al. (2006). Basic idea of B1 index is to calculate the
11 distance between the two strands, when the leading and lagging strands
12 are plotted in a coordinate system with axes representing G/(G+C) and
13 A/(A+T), using the third codon position of genes. This index measures the
14 degree of replication-induced bias from Chargaff's second parity rule.
15 Rocha et al. modified B1 index to only use >fourfold degenerate codons,
16 and to use T/(A+T) in place of A/(A+T).
17
18 G-language SOAP service is provided by the
19 Institute for Advanced Biosciences, Keio University.
20 The original web service is located at the following URL:
21
22 http://www.g-language.org/wiki/soap
23
24 WSDL(RPC/Encoded) file is located at:
25
26 http://soap.g-language.org/g-language.wsdl
27
28 Documentation on G-language Genome Analysis Environment methods are
29 provided at the Document Center
30
31 http://ws.g-language.org/gdoc/
32
33 Usage
34
35 Here is a sample session with gb1
36
37 % gb1 refseqn:NC_000913
38 Calculate strand bias of bacterial genome using B1 index
39 Program compseq output file [nc_000913.gb1]:
40
41 Go to the input files for this example
42 Go to the output files for this example
43
44 Command line arguments
45
46 Standard (Mandatory) qualifiers:
47 [-sequence] seqall Nucleotide sequence(s) filename and optional
48 format, or reference (input USA)
49 [-outfile] outfile [*.gb1] Program compseq output file
50
51 Additional (Optional) qualifiers: (none)
52 Advanced (Unprompted) qualifiers:
53 -method selection [rocha] Choose method of 'lobry' or 'rocha'
54 -[no]accid boolean [Y] Include to use sequence accession ID as
55 query
56
57 Associated qualifiers:
58
59 "-sequence" associated qualifiers
60 -sbegin1 integer Start of each sequence to be used
61 -send1 integer End of each sequence to be used
62 -sreverse1 boolean Reverse (if DNA)
63 -sask1 boolean Ask for begin/end/reverse
64 -snucleotide1 boolean Sequence is nucleotide
65 -sprotein1 boolean Sequence is protein
66 -slower1 boolean Make lower case
67 -supper1 boolean Make upper case
68 -scircular1 boolean Sequence is circular
69 -sformat1 string Input sequence format
70 -iquery1 string Input query fields or ID list
71 -ioffset1 integer Input start position offset
72 -sdbname1 string Database name
73 -sid1 string Entryname
74 -ufo1 string UFO features
75 -fformat1 string Features format
76 -fopenfile1 string Features file name
77
78 "-outfile" associated qualifiers
79 -odirectory2 string Output directory
80
81 General qualifiers:
82 -auto boolean Turn off prompts
83 -stdout boolean Write first file to standard output
84 -filter boolean Read first file from standard input, write
85 first file to standard output
86 -options boolean Prompt for standard and additional values
87 -debug boolean Write debug output to program.dbg
88 -verbose boolean Report some/full command line options
89 -help boolean Report command line options and exit. More
90 information on associated and general
91 qualifiers can be found with -help -verbose
92 -warning boolean Report warnings
93 -error boolean Report errors
94 -fatal boolean Report fatal errors
95 -die boolean Report dying program messages
96 -version boolean Report version number and exit
97
98 Input file format
99
100 The database definitions for following commands are available at
101 http://soap.g-language.org/kbws/embossrc
102
103 gb1 reads one or more nucleotide sequences.
104
105 Output file format
106
107 The output from gb1 is to a plain text file.
108
109 File: nc_000913.gb1
110
111 Sequence: NC_000913 B1: 0.0630702874711314
112
113
114 Data files
115
116 None.
117
118 Notes
119
120 None.
121
122 References
123
124 Lobry JR and Sueoka N (2002) Asymmetric directional mutation pressures in
125 bacteria, Genome Biology, 3(10):0058
126
127 Rocha EPC et al. (2006) Similar compositional biases are caused by very
128 different mutational effects, Genome Research, 16:1537-1547
129
130 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
131 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
132 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
133
134 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
135 large-scale analysis of high-throughput omics data, J. Pest Sci.,
136 31, 7.
137
138 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
139 Analysis Environment with REST and SOAP Web Service Interfaces,
140 Nucleic Acids Res., 38, W700-W705.
141
142 Warnings
143
144 None.
145
146 Diagnostic Error Messages
147
148 None.
149
150 Exit status
151
152 It always exits with a status of 0.
153
154 Known bugs
155
156 None.
157
158 See also
159
160 gb2 Calculate strand bias of bacterial genome using B2 index
161 gdeltagcskew Calculate strand bias of bacterial genome using delta GC skew
162 index
163 ggcsi GC Skew Index: an index for strand-specefic mutational bias
164 gldabias Calculate strand bias of bacterial genome using linear
165 discriminant analysis (LDA)
166
167 Author(s)
168
169 Hidetoshi Itaya (celery@g-language.org)
170 Institute for Advanced Biosciences, Keio University
171 252-0882 Japan
172
173 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
174 Institute for Advanced Biosciences, Keio University
175 252-0882 Japan
176
177 History
178
179 2012 - Written by Hidetoshi Itaya
180 2013 - Fixed by Hidetoshi Itaya
181
182 Target users
183
184 This program is intended to be used by everyone and everything, from
185 naive users to embedded scripts.
186
187 Comments
188
189 None.
190