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

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1 gsvalue
2 Function
3
4 Calculate the strength of selected codon usage bias (S)
5
6 Description
7
8 gsvalue calculates the strength of selected codon usage bias (S), also
9 known as Sharp's S index. Using four codon pairs that are recognized by the
10 same tRNA anticodon, namely, Phe(UUC and UUU), Ile(AUC and AUU), Tyr(UAC and
11 UAU), and Asn(AAC and AAU), since the former in each of the pairs has
12 stronger Watson-Crick pairing, selection towards the former codon can be
13 observed for highly expressed genes. S index is therefore the weighted
14 average of such bias, giving an over-all value for a genome, indicating its
15 strength of selected codon usage bias. See Sharp et al. (2005) for details.
16 Sharp originally defined 40 genes as the highly expressed gene group, with
17 tufA, tsf, fusA, rplA-rplF, rplI-rplT, rpsB-rpsT. Since the identificaiton
18 of these genes is not convenient for computational automation, by default,
19 this method uses ribosomal proteins as the highly expressed gene group,
20 as used by Viera-silva and Rocha (2010).
21 However, Sharp's gene group can be optionally used with -sharp option.
22 With this option, all of the 40 genes must be named accordingly in the given
23 genome file.
24
25 G-language SOAP service is provided by the
26 Institute for Advanced Biosciences, Keio University.
27 The original web service is located at the following URL:
28
29 http://www.g-language.org/wiki/soap
30
31 WSDL(RPC/Encoded) file is located at:
32
33 http://soap.g-language.org/g-language.wsdl
34
35 Documentation on G-language Genome Analysis Environment methods are
36 provided at the Document Center
37
38 http://ws.g-language.org/gdoc/
39
40 Usage
41
42 Here is a sample session with gsvalue
43
44 % gsvalue refseqn:NC_000913
45 Calculate the strength of selected codon usage bias (S)
46 Codon usage output file [nc_000913.gsvalue]:
47
48 Go to the input files for this example
49 Go to the output files for this example
50
51 Command line arguments
52
53 Standard (Mandatory) qualifiers:
54 [-sequence] seqall Nucleotide sequence(s) filename and optional
55 format, or reference (input USA)
56 [-outfile] outfile [*.gsvalue] Codon usage output file
57
58 Additional (Optional) qualifiers: (none)
59 Advanced (Unprompted) qualifiers:
60 -sharp boolean [N] Include to use the 40 genes used by
61 Sharp instead of ribosomal proteins
62 -[no]accid boolean [Y] Include to use sequence accession ID as
63 query
64
65 Associated qualifiers:
66
67 "-sequence" associated qualifiers
68 -sbegin1 integer Start of each sequence to be used
69 -send1 integer End of each sequence to be used
70 -sreverse1 boolean Reverse (if DNA)
71 -sask1 boolean Ask for begin/end/reverse
72 -snucleotide1 boolean Sequence is nucleotide
73 -sprotein1 boolean Sequence is protein
74 -slower1 boolean Make lower case
75 -supper1 boolean Make upper case
76 -scircular1 boolean Sequence is circular
77 -sformat1 string Input sequence format
78 -iquery1 string Input query fields or ID list
79 -ioffset1 integer Input start position offset
80 -sdbname1 string Database name
81 -sid1 string Entryname
82 -ufo1 string UFO features
83 -fformat1 string Features format
84 -fopenfile1 string Features file name
85
86 "-outfile" associated qualifiers
87 -odirectory2 string Output directory
88
89 General qualifiers:
90 -auto boolean Turn off prompts
91 -stdout boolean Write first file to standard output
92 -filter boolean Read first file from standard input, write
93 first file to standard output
94 -options boolean Prompt for standard and additional values
95 -debug boolean Write debug output to program.dbg
96 -verbose boolean Report some/full command line options
97 -help boolean Report command line options and exit. More
98 information on associated and general
99 qualifiers can be found with -help -verbose
100 -warning boolean Report warnings
101 -error boolean Report errors
102 -fatal boolean Report fatal errors
103 -die boolean Report dying program messages
104 -version boolean Report version number and exit
105
106 Input file format
107
108 The database definitions for following commands are available at
109 http://soap.g-language.org/kbws/embossrc
110
111 gsvalue reads one or more nucleotide sequences.
112
113 Output file format
114
115 The output from gsvalue is to a plain text file.
116
117 File: nc_000913.gsvalue
118
119 Sequence: NC_000913 S-value: 1.23467100598485
120
121
122 Data files
123
124 None.
125
126 Notes
127
128 None.
129
130 References
131
132 Sharp PM et al. (2005) "Variation in the strength of selected codon usage
133 bias among bacteria", Nucleic Acids Research, 33(4):1141-1153
134
135 Vieira-Silva S and Rocha EPC (2010) "The systemic imprint of growth and its
136 uses in ecological (meta)genomics", PLoS Genetics, 6(1):e1000808
137
138 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
139 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
140 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
141
142 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
143 large-scale analysis of high-throughput omics data, J. Pest Sci.,
144 31, 7.
145
146 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
147 Analysis Environment with REST and SOAP Web Service Interfaces,
148 Nucleic Acids Res., 38, W700-W705.
149
150 Warnings
151
152 None.
153
154 Diagnostic Error Messages
155
156 None.
157
158 Exit status
159
160 It always exits with a status of 0.
161
162 Known bugs
163
164 None.
165
166 See also
167
168 gcbi Calculates the codon bias index (CBI)
169 gdelta_enc Calculate the codon usage bias related to translation optimization (delta ENC)
170 gicdi Calculates the intrinsic codon deviation index (ICDI)
171
172 Author(s)
173
174 Hidetoshi Itaya (celery@g-language.org)
175 Institute for Advanced Biosciences, Keio University
176 252-0882 Japan
177
178 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
179 Institute for Advanced Biosciences, Keio University
180 252-0882 Japan
181
182 History
183
184 2012 - Written by Hidetoshi Itaya
185 2013 - Fixed by Hidetoshi Itaya
186
187 Target users
188
189 This program is intended to be used by everyone and everything, from
190 naive users to embedded scripts.
191
192 Comments
193
194 None.
195