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

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date Fri, 26 Jun 2015 05:19:29 -0400
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1 gwvalue
2 Function
3
4 Calculate the 'relative adaptiveness of each codon' (W)
5
6 Description
7
8 gwvalue calculates the 'relative adaptiveness of each codon' (W value)
9 which is essential in CAI analysis. W value is calculated by setting the
10 best codon to 1 and calculating the proportion of the other codons.
11
12 G-language SOAP service is provided by the
13 Institute for Advanced Biosciences, Keio University.
14 The original web service is located at the following URL:
15
16 http://www.g-language.org/wiki/soap
17
18 WSDL(RPC/Encoded) file is located at:
19
20 http://soap.g-language.org/g-language.wsdl
21
22 Documentation on G-language Genome Analysis Environment methods are
23 provided at the Document Center
24
25 http://ws.g-language.org/gdoc/
26
27 Usage
28
29 Here is a sample session with gwvalue
30
31 % gwvalue refseqn:NC_000913
32 Calculate the 'relative adaptiveness of each codon' (W)
33 Codon usage output file [nc_000913.gwvalue]:
34
35 Go to the input files for this example
36 Go to the output files for this example
37
38 Command line arguments
39
40 Standard (Mandatory) qualifiers:
41 [-sequence] seqall Nucleotide sequence(s) filename and optional
42 format, or reference (input USA)
43 [-outfile] outfile [*.gwvalue] Codon usage output file
44
45 Additional (Optional) qualifiers: (none)
46 Advanced (Unprompted) qualifiers:
47 -include string [ribosomal.*protein] Regular expression to
48 include genes in a reference set a reference
49 set in several studies are in-built 1:
50 Nakamura and Tabata, 2: Sharp and Li, 3:
51 Sakai et al. (Any string)
52 -exclude string [[Mm]itochondrial] Regular expression to
53 exclude genes from a reference set (Any
54 string)
55 -[no]accid boolean [Y] Include to use sequence accession ID as
56 query
57
58 Associated qualifiers:
59
60 "-sequence" associated qualifiers
61 -sbegin1 integer Start of each sequence to be used
62 -send1 integer End of each sequence to be used
63 -sreverse1 boolean Reverse (if DNA)
64 -sask1 boolean Ask for begin/end/reverse
65 -snucleotide1 boolean Sequence is nucleotide
66 -sprotein1 boolean Sequence is protein
67 -slower1 boolean Make lower case
68 -supper1 boolean Make upper case
69 -scircular1 boolean Sequence is circular
70 -sformat1 string Input sequence format
71 -iquery1 string Input query fields or ID list
72 -ioffset1 integer Input start position offset
73 -sdbname1 string Database name
74 -sid1 string Entryname
75 -ufo1 string UFO features
76 -fformat1 string Features format
77 -fopenfile1 string Features file name
78
79 "-outfile" associated qualifiers
80 -odirectory2 string Output directory
81
82 General qualifiers:
83 -auto boolean Turn off prompts
84 -stdout boolean Write first file to standard output
85 -filter boolean Read first file from standard input, write
86 first file to standard output
87 -options boolean Prompt for standard and additional values
88 -debug boolean Write debug output to program.dbg
89 -verbose boolean Report some/full command line options
90 -help boolean Report command line options and exit. More
91 information on associated and general
92 qualifiers can be found with -help -verbose
93 -warning boolean Report warnings
94 -error boolean Report errors
95 -fatal boolean Report fatal errors
96 -die boolean Report dying program messages
97 -version boolean Report version number and exit
98
99 Input file format
100
101 The database definitions for following commands are available at
102 http://soap.g-language.org/kbws/embossrc
103
104 gwvalue reads one or more nucleotide sequences.
105
106 Output file format
107
108 The output from gwvalue is to a plain text file.
109
110 File: nc_000913.gwvalue
111
112 Sequence: NC_000913
113 Reference set of highly expressed genes
114 product
115 30S ribosomal subunit protein S20
116 30S ribosomal subunit protein S2
117 ribosomal protein S12 methylthiotransferase; radical SAM superfamily
118 ribosomal protein S6 modification protein
119 30S ribosomal subunit protein S1
120 ribosomal-protein-S5-alanine N-acetyltransferase
121 50S ribosomal subunit protein L32
122
123 [Part of this file has been deleted for brevity]
124
125 T,acc,1.0000
126 T,acg,0.2234
127 T,act,0.9734
128 V,gta,0.4960
129 V,gtc,0.2281
130 V,gtg,0.3422
131 V,gtt,1.0000
132 W,tgg,1.0000
133 Y,tac,1.0000
134 Y,tat,0.5310
135
136
137 Data files
138
139 None.
140
141 Notes
142
143 None.
144
145 References
146
147 Sharp PM et al. (2005) Variation in the strength of selected codon usage
148 bias among bacteria, Nucleic Acids Res. 33(4):1141-1153
149
150 Sakai et al. (2001) Correlation between Shine--Dalgarno sequence
151 conservation and codon usage of bacterial genes, J.Mol.Evol. 52:164-170.
152
153 Nakamura and Tabata (1997) Codon-anticodon assignment and detection of
154 codon usage trends in seven microbial genomes, Microb.Comp.Genomics
155 2:299-312.
156
157 Sharp and Li (1987) The codon Adaptation Index--a measure of directional
158 synonymous codon usage bias, and its potential applications, Nucleic
159 Acids Res. 15:1281-1295.
160
161 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
162 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
163 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
164
165 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
166 large-scale analysis of high-throughput omics data, J. Pest Sci.,
167 31, 7.
168
169 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
170 Analysis Environment with REST and SOAP Web Service Interfaces,
171 Nucleic Acids Res., 38, W700-W705.
172
173 Warnings
174
175 None.
176
177 Diagnostic Error Messages
178
179 None.
180
181 Exit status
182
183 It always exits with a status of 0.
184
185 Known bugs
186
187 None.
188
189 See also
190
191 genc Calculate the effective number of codons (Nc)
192 gew Calculate a measure of synonymous codon usage evenness (Ew)
193 gfop Calculate the frequency of optimal codons (Fop)
194 gscs Calculates the scaled chi-square
195
196 Author(s)
197
198 Hidetoshi Itaya (celery@g-language.org)
199 Institute for Advanced Biosciences, Keio University
200 252-0882 Japan
201
202 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
203 Institute for Advanced Biosciences, Keio University
204 252-0882 Japan
205
206 History
207
208 2012 - Written by Hidetoshi Itaya
209 2013 - Fixed by Hidetoshi Itaya
210
211 Target users
212
213 This program is intended to be used by everyone and everything, from
214 naive users to embedded scripts.
215
216 Comments
217
218 None.
219